An External Archive-Guided Multiobjective Particle Swarm Optimization Algorithm.

PubMed

Zhu, Qingling; Lin, Qiuzhen; Chen, Weineng; Wong, Ka-Chun; Coello Coello, Carlos A; Li, Jianqiang; Chen, Jianyong; Zhang, Jun

2017-09-01

The selection of swarm leaders (i.e., the personal best and global best), is important in the design of a multiobjective particle swarm optimization (MOPSO) algorithm. Such leaders are expected to effectively guide the swarm to approach the true Pareto optimal front. In this paper, we present a novel external archive-guided MOPSO algorithm (AgMOPSO), where the leaders for velocity update are all selected from the external archive. In our algorithm, multiobjective optimization problems (MOPs) are transformed into a set of subproblems using a decomposition approach, and then each particle is assigned accordingly to optimize each subproblem. A novel archive-guided velocity update method is designed to guide the swarm for exploration, and the external archive is also evolved using an immune-based evolutionary strategy. These proposed approaches speed up the convergence of AgMOPSO. The experimental results fully demonstrate the superiority of our proposed AgMOPSO in solving most of the test problems adopted, in terms of two commonly used performance measures. Moreover, the effectiveness of our proposed archive-guided velocity update method and immune-based evolutionary strategy is also experimentally validated on more than 30 test MOPs.

Assessment of configurations and chemistries of bridged nucleic acids-containing oligomers as external guide sequences: a methodology for inhibition of expression of antibiotic resistance genes

PubMed Central

Jackson, Alexis; Jani, Saumya; Davies-Sala, Carol; Soler-Bistué, Alfonso J. C.; Zorreguieta, Angeles; Tolmasky, Marcelo E.

2016-01-01

External guide sequences (EGSs) are short antisense oligoribonucleotides that elicit RNase P-mediated cleavage of a target mRNA, which results in inhibition of gene expression. EGS technology is used to inhibit expression of a wide variety of genes, a strategy that may lead to development of novel treatments of numerous diseases, including multidrug-resistant bacterial and viral infections. Successful development of EGS technology depends on finding nucleotide analogs that resist degradation by nucleases present in biological fluids and the environment but still elicit RNase P-mediated degradation when forming a duplex with a target mRNA. Previous results suggested that locked nucleic acids (LNA)/DNA chimeric oligomers have these properties. LNA are now considered the first generation of compounds collectively known as bridged nucleic acids (BNAs) – modified ribonucleotides that contain a bridge at the 2ʹ,4ʹ-position of the ribose. LNA and the second-generation BNA, known as BNANC, differ in the chemical nature of the bridge. Chimeric oligomers containing LNA or BNANC and deoxynucleotide monomers in different configurations are nuclease resistant and could be excellent EGS compounds. However, not all configurations may be equally active as EGSs. RNase P cleavage assays comparing LNA/DNA and BNANC/DNA chimeric oligonucleotides that share identical nucleotide sequence but with different configurations were carried out using as target the amikacin resistance aac(6ʹ)-Ib mRNA. LNA/DNA gapmers with 5 and 3/4 LNA residues at the 5ʹ- and 3ʹ-ends, respectively, were the most efficient EGSs while all BNANC/DNA gapmers showed very poor activity. When the most efficient LNA/DNA gapmer was covalently bound to a cell-penetrating peptide, the hybrid compound conserved the EGS activity as determined by RNase P cleavage assays and reduced the levels of resistance to amikacin when added to Acinetobacter baumannii cells in culture, an indication of cellular uptake and biological activity. PMID:27857983

Simultaneous orthogonal plane imaging.

PubMed

Mickevicius, Nikolai J; Paulson, Eric S

2017-11-01

Intrafraction motion can result in a smearing of planned external beam radiation therapy dose distributions, resulting in an uncertainty in dose actually deposited in tissue. The purpose of this paper is to present a pulse sequence that is capable of imaging a moving target at a high frame rate in two orthogonal planes simultaneously for MR-guided radiotherapy. By balancing the zero gradient moment on all axes, slices in two orthogonal planes may be spatially encoded simultaneously. The orthogonal slice groups may be acquired with equal or nonequal echo times. A Cartesian spoiled gradient echo simultaneous orthogonal plane imaging (SOPI) sequence was tested in phantom and in vivo. Multiplexed SOPI acquisitions were performed in which two parallel slices were imaged along two orthogonal axes simultaneously. An autocalibrating phase-constrained 2D-SENSE-GRAPPA (generalized autocalibrating partially parallel acquisition) algorithm was implemented to reconstruct the multiplexed data. SOPI images without intraslice motion artifacts were reconstructed at a maximum frame rate of 8.16 Hz. The 2D-SENSE-GRAPPA reconstruction separated the parallel slices aliased along each orthogonal axis. The high spatiotemporal resolution provided by SOPI has the potential to be beneficial for intrafraction motion management during MR-guided radiation therapy or other MRI-guided interventions. Magn Reson Med 78:1700-1710, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Behavioral and Nondirective Guided Self-Help for Parents of Children with Externalizing Behavior: Mediating Mechanisms in a Head-To-Head Comparison.

PubMed

Katzmann, Josepha; Hautmann, Christopher; Greimel, Lisa; Imort, Stephanie; Pinior, Julia; Scholz, Kristin; Döpfner, Manfred

2017-05-01

Parent training (PT) delivered as a guided self-help intervention may be a cost- and time-effective intervention in the treatment of children with externalizing disorders. In face-to-face PT, parenting strategies have repeatedly been identified as mediating mechanisms for the decrease of children's problem behavior. Few studies have examined possible mediating effects in guided self-help interventions for parents. The present study aimed to investigate possible mediating variables of a behaviorally oriented guided self-help program for parents of children with externalizing problems compared to a nondirective intervention in a clinical sample. A sample of 110 parents of children with externalizing disorders (80 % boys) were randomized to either a behaviorally oriented or a nondirective guided self-help program. Four putative mediating variables were examined simultaneously in a multiple mediation model using structural equation modelling. The outcomes were child symptoms of ADHD and ODD as well as child externalizing problems, assessed at posttreatment. Analyses showed a significant indirect effect for dysfunctional parental attributions in favor of the group receiving the behavioral program, and significant effects of the behavioral program on positive and negative parenting and parental self-efficacy, compared to the nondirective intervention. Our results indicate that a decrease of dysfunctional parental attributions leads to a decrease of child externalizing problems when parents take part in a behaviorally oriented guided self-help program. However, none of the putative mediating variables could explain the decrease in child externalizing behavior problems in the nondirective group. A change in dysfunctional parental attributions should be considered as a possible mediator in the context of PT.

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

A population study of the minicircles in Trypanosoma cruzi: predicting guide RNAs in the absence of empirical RNA editing.

PubMed

Thomas, Sean; Martinez, L L Isadora Trejo; Westenberger, Scott J; Sturm, Nancy R

2007-05-24

The structurally complex network of minicircles and maxicircles comprising the mitochondrial DNA of kinetoplastids mirrors the complexity of the RNA editing process that is required for faithful expression of encrypted maxicircle genes. Although a few of the guide RNAs that direct this editing process have been discovered on maxicircles, guide RNAs are mostly found on the minicircles. The nuclear and maxicircle genomes have been sequenced and assembled for Trypanosoma cruzi, the causative agent of Chagas disease, however the complement of 1.4-kb minicircles, carrying four guide RNA genes per molecule in this parasite, has been less thoroughly characterised. Fifty-four CL Brener and 53 Esmeraldo strain minicircle sequence reads were extracted from T. cruzi whole genome shotgun sequencing data. With these sequences and all published T. cruzi minicircle sequences, 108 unique guide RNAs from all known T. cruzi minicircle sequences and two guide RNAs from the CL Brener maxicircle were predicted using a local alignment algorithm and mapped onto predicted or experimentally determined sequences of edited maxicircle open reading frames. For half of the sequences no statistically significant guide RNA could be assigned. Likely positions of these unidentified gRNAs in T. cruzi minicircle sequences are estimated using a simple Hidden Markov Model. With the local alignment predictions as a standard, the HMM had an ~85% chance of correctly identifying at least 20 nucleotides of guide RNA from a given minicircle sequence. Inter-minicircle recombination was documented. Variable regions contain species-specific areas of distinct nucleotide preference. Two maxicircle guide RNA genes were found. The identification of new minicircle sequences and the further characterization of all published minicircles are presented, including the first observation of recombination between minicircles. Extrapolation suggests a level of 4% recombinants in the population, supporting a relatively high recombination rate that may serve to minimize the persistence of gRNA pseudogenes. Characteristic nucleotide preferences observed within variable regions provide potential clues regarding the transcription and maturation of T. cruzi guide RNAs. Based on these preferences, a method of predicting T. cruzi guide RNAs using only primary minicircle sequence data was created.

Magnetic Resonance Imaging–Guided versus Surrogate-Based Motion Tracking in Liver Radiation Therapy: A Prospective Comparative Study

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

Paganelli, Chiara, E-mail: chiara.paganelli@polimi.it; Seregni, Matteo; Fattori, Giovanni

Purpose: This study applied automatic feature detection on cine–magnetic resonance imaging (MRI) liver images in order to provide a prospective comparison between MRI-guided and surrogate-based tracking methods for motion-compensated liver radiation therapy. Methods and Materials: In a population of 30 subjects (5 volunteers plus 25 patients), 2 oblique sagittal slices were acquired across the liver at high temporal resolution. An algorithm based on scale invariant feature transform (SIFT) was used to extract and track multiple features throughout the image sequence. The position of abdominal markers was also measured directly from the image series, and the internal motion of each featuremore » was quantified through multiparametric analysis. Surrogate-based tumor tracking with a state-of-the-art external/internal correlation model was simulated. The geometrical tracking error was measured, and its correlation with external motion parameters was also investigated. Finally, the potential gain in tracking accuracy relying on MRI guidance was quantified as a function of the maximum allowed tracking error. Results: An average of 45 features was extracted for each subject across the whole liver. The multi-parametric motion analysis reported relevant inter- and intrasubject variability, highlighting the value of patient-specific and spatially-distributed measurements. Surrogate-based tracking errors (relative to the motion amplitude) were were in the range 7% to 23% (1.02-3.57mm) and were significantly influenced by external motion parameters. The gain of MRI guidance compared to surrogate-based motion tracking was larger than 30% in 50% of the subjects when considering a 1.5-mm tracking error tolerance. Conclusions: Automatic feature detection applied to cine-MRI allows detailed liver motion description to be obtained. Such information was used to quantify the performance of surrogate-based tracking methods and to provide a prospective comparison with respect to MRI-guided radiation therapy, which could support the definition of patient-specific optimal treatment strategies.« less

[Methodological quality of an article on the treatment of gastric cancer adopted as protocol by some Chilean hospitals].

PubMed

Manterola, Carlos; Torres, Rodrigo; Burgos, Luis; Vial, Manuel; Pineda, Viviana

2006-07-01

Surgery is a curative treatment for gastric cancer (GC). As relapse is frequent, adjuvant therapies such as postoperative chemo radiotherapy have been tried. In Chile, some hospitals adopted Macdonald's study as a protocol for the treatment of GC. To determine methodological quality and internal and external validity of the Macdonald study. Three instruments were applied that assess methodological quality. A critical appraisal was done and the internal and external validity of the methodological quality was analyzed with two scales: MINCIR (Methodology and Research in Surgery), valid for therapy studies and CONSORT (Consolidated Standards of Reporting Trials), valid for randomized controlled trials (RCT). Guides and scales were applied by 5 researchers with training in clinical epidemiology. The reader's guide verified that the Macdonald study was not directed to answer a clearly defined question. There was random assignment, but the method used is not described and the patients were not considered until the end of the study (36% of the group with surgery plus chemo radiotherapy did not complete treatment). MINCIR scale confirmed a multicentric RCT, not blinded, with an unclear randomized sequence, erroneous sample size estimation, vague objectives and no exclusion criteria. CONSORT system proved the lack of working hypothesis and specific objectives as well as an absence of exclusion criteria and identification of the primary variable, an imprecise estimation of sample size, ambiguities in the randomization process, no blinding, an absence of statistical adjustment and the omission of a subgroup analysis. The instruments applied demonstrated methodological shortcomings that compromise the internal and external validity of the.

Overhead guide sign retroreflectivity and illumination.

DOT National Transportation Integrated Search

2015-01-01

Roadway guide sign visibility during darkness is fundamental to driver safety, especially elderly drivers. Guide : sign visibility can be improved by external sign illumination or the use of retroreflective sheeting on signs. Because : energy conserv...

Career Academy Course Sequences.

ERIC Educational Resources Information Center

Markham, Thom; Lenz, Robert

This career academy course sequence guide is designed to give teachers a quick overview of the course sequences of well-known career academy and career pathway programs from across the country. The guide presents a variety of sample course sequences for the following academy themes: (1) arts and communication; (2) business and finance; (3)…

Memory-guided selective attention: Single experiences with conflict have long-lasting effects on cognitive control.

PubMed

Brosowsky, Nicholaus P; Crump, Matthew J C

2018-05-17

Adjustments in cognitive control, as measured by congruency sequence effects, are thought to be influenced by both external stimuli and internal goals. However, this dichotomy has often overshadowed the potential contribution of past experience stored in memory. Here, we examine the role of long-term episodic memory in guiding selective attention. Our aim was to demonstrate new evidence that selective attention can be modulated by long-term retrieval of stimulus-specific attentional control settings. All the experiments used a modified flanker task involving multiple unique stimuli. Critically, each stimulus was only presented twice during the experiment: first as a prime, and second as a probe. Experiments 1 and 2 varied the number of intervening trials between prime and probe and manipulated the amount of conflict using a secondary task. Experiment 3 ensured that specific colors assigned to prime stimuli were not repeated when presented as probes. Across both Experiments 1 and 2, we consistently found smaller congruency effects on probe trials when its associated prime trial was incongruent compared with congruent, demonstrating long-term congruency sequence effects. However, Experiment 3 showed no evidence for long-term effects. These findings suggest long-term preservation of selective attention processing at the episodic level, and implicate a role for memory in updating cognitive control. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Photographic guide of selected external defect indicators and associated internal defects in yellow birch

Treesearch

Everette D. Rast; John A. Beaton; David L. Sonderman

1991-01-01

To properly classify or grade logs or trees, one must be able to correctly identify defect indicators and assess the effect of the underlying defect on possible end products. This guide assists the individual in identifying the surface defect indicator and shows the progressive stages of the defect throughout its development for yellow birch. Eleven types of external...

Photographic guide of selected external defect indicators and associated internal defects in sugar maple

Treesearch

Everette D. Rast; John A. Beaton; David L. Sonderman

1991-01-01

To properly classify or grade logs or trees, one must be able to correctly identify defect indicators and assess the effect of the underlying defect on possible end products. This guide assists the individual in identifying the surface defect indicator and shows the progressive stages of the defect throughout its development for sugar maple. Eleven types of external...

Photographic guide of selected external defect indicators and associated internal defects in yellow-poplar

Treesearch

Everette D. Rast; John A. Beaton; David L. Sonderman

1991-01-01

To properly classify or grade logs or trees, one must be able to correctly identify defect indicators and assess the effect of the underlying defect on possible end products. This guide assists the individual in identifying the surface defect indicator and shows the progressive stages of the defect throughout its development for yellow-poplar. Twelve types of external...

The Guiding Effects of a Critical Reading Program on the Use of External Reading Strategies When Confronting an Ironical Text

ERIC Educational Resources Information Center

Karabay, Aysegul

2015-01-01

This study employed a sample of 60 pre-service teachers to examine the guiding effects of understanding critical reading theories on using external reading strategies such as note-taking and underlining when confronting an ironical literary text. The study broke down the teachers into one control group of 30 teachers and one experimental group of…

Optical properties of antiferromagnetic/ion-crystal superlattices

NASA Astrophysics Data System (ADS)

Ta, Jin-Xing; Song, Yu-Ling; Wang, Xuan-Zhang

2012-01-01

Transmission, refraction and absorption properties of an antiferromagnetic/ion-crystal superlattice are investigated. The transmission spectra based on FeF2/TlBr superlattices reveal that there exist two intriguing guided modes in a wide stop band. Additionally, FeF2/TlBr superlattices possess either the negative refraction or the quasi left-handedness, or even simultaneously hold them at certain frequencies of two guided modes, which require both negative magnetic permeability of antiferromagnetic layers and negative permittivity of ion-crystal layers. Frequency regimes of the guided modes will be dependent on the magnitude of the external magnetic field. Therefore, handedness and refraction properties of the system can be manipulated by modifying the external magnetic field. Absorption spectra exhibit that absorption corresponding to guided modes is noticeable.

Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) Version 3.0 User Guide

EPA Science Inventory

User Guide to describe the complete functionality of the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) Version 3.0 online tool. The US Environmental Protection Agency Sequence Alignment to Predict Across Species Susceptibility tool (SeqAPASS; https://seqa...

Abnormal externally guided movement preparation in recent-onset schizophrenia is associated with impaired selective attention to external input.

PubMed

Smid, Henderikus G O M; Westenbroek, Joanna M; Bruggeman, Richard; Knegtering, Henderikus; Van den Bosch, Robert J

2009-11-30

Several theories propose that the primary cognitive impairment in schizophrenia concerns a deficit in the processing of external input information. There is also evidence, however, for impaired motor preparation in schizophrenia. This provokes the question whether the impaired motor preparation in schizophrenia is a secondary consequence of disturbed (selective) processing of the input needed for that preparation, or an independent primary deficit. The aim of the present study was to discriminate between these hypotheses, by investigating externally guided movement preparation in relation to selective stimulus processing. The sample comprised 16 recent-onset schizophrenia patients and 16 controls who performed a movement-precuing task. In this task, a precue delivered information about one, two or no parameters of a movement summoned by a subsequent stimulus. Performance measures and measures derived from the electroencephalogram showed that patients yielded smaller benefits from the precues and showed less cue-based preparatory activity in advance of the imperative stimulus than the controls, suggesting a response preparation deficit. However, patients also showed less activity reflecting selective attention to the precue. We therefore conclude that the existing evidence for an impairment of externally guided motor preparation in schizophrenia is most likely due to a deficit in selective attention to the external input, which lends support to theories proposing that the primary cognitive deficit in schizophrenia concerns the processing of input information.

mrtailor: a tool for PDB-file preparation for the generation of external restraints.

PubMed

Gruene, Tim

2013-09-01

Model building starting from, for example, a molecular-replacement solution with low sequence similarity introduces model bias, which can be difficult to detect, especially at low resolution. The program mrtailor removes low-similarity regions from a template PDB file according to sequence similarity between the target sequence and the template sequence and maps the target sequence onto the PDB file. The modified PDB file can be used to generate external restraints for low-resolution refinement with reduced model bias and can be used as a starting point for model building and refinement. The program can call ProSMART [Nicholls et al. (2012), Acta Cryst. D68, 404-417] directly in order to create external restraints suitable for REFMAC5 [Murshudov et al. (2011), Acta Cryst. D67, 355-367]. Both a command-line version and a GUI exist.

Health Occupations: Scope and Sequence.

ERIC Educational Resources Information Center

Nashville - Davidson County Metropolitan Public Schools, TN.

This guide, which was written as an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System, outlines the suggested scope and sequence of a 3-year program in health occupations. The guide consists of a course description; general course…

VOE Computer Programming: Scope and Sequence.

ERIC Educational Resources Information Center

Nashville - Davidson County Metropolitan Public Schools, TN.

This guide, which was written as an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System, outlines the suggested scope and sequence of a 3-year program in computer programming. The guide consists of a course description; general course…

Urban Horticulture: Scope and Sequence.

ERIC Educational Resources Information Center

Nashville - Davidson County Metropolitan Public Schools, TN.

This guide, which was written as an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System, outlines the suggested scope and sequence of a 4-year program in urban horticulture. The guide consists of a course description; general course…

VOE Accounting: Scope and Sequence.

ERIC Educational Resources Information Center

Nashville - Davidson County Metropolitan Public Schools, TN.

This guide, which was written as an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System, outlines the suggested scope and sequence of a 2-year program in accounting. The guide consists of a course description; general course objectives;…

Agriculture: Scope and Sequence.

ERIC Educational Resources Information Center

Nashville - Davidson County Metropolitan Public Schools, TN.

This guide, which was written as an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System, outlines the suggested scope and sequence of a 3-year program in agriculture. The guide consists of a course description; general course objectives;…

Advanced Endoscopic Navigation: Surgical Big Data, Methodology, and Applications.

PubMed

Luo, Xiongbiao; Mori, Kensaku; Peters, Terry M

2018-06-04

Interventional endoscopy (e.g., bronchoscopy, colonoscopy, laparoscopy, cystoscopy) is a widely performed procedure that involves either diagnosis of suspicious lesions or guidance for minimally invasive surgery in a variety of organs within the body cavity. Endoscopy may also be used to guide the introduction of certain items (e.g., stents) into the body. Endoscopic navigation systems seek to integrate big data with multimodal information (e.g., computed tomography, magnetic resonance images, endoscopic video sequences, ultrasound images, external trackers) relative to the patient's anatomy, control the movement of medical endoscopes and surgical tools, and guide the surgeon's actions during endoscopic interventions. Nevertheless, it remains challenging to realize the next generation of context-aware navigated endoscopy. This review presents a broad survey of various aspects of endoscopic navigation, particularly with respect to the development of endoscopic navigation techniques. First, we investigate big data with multimodal information involved in endoscopic navigation. Next, we focus on numerous methodologies used for endoscopic navigation. We then review different endoscopic procedures in clinical applications. Finally, we discuss novel techniques and promising directions for the development of endoscopic navigation.

Marketing and Distributive Education: Scope and Sequence.

ERIC Educational Resources Information Center

Nashville - Davidson County Metropolitan Public Schools, TN.

This guide, which was written as an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System, outlines the suggested scope and sequence of a 2-year program in marketing and distributive education. The guide consists of a course description;…

Industrial Cooperative Education Co-op: Scope and Sequence.

ERIC Educational Resources Information Center

Nashville - Davidson County Metropolitan Public Schools, TN.

This guide, which was written as an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System, outlines the suggested scope and sequence of a 2-year cooperative program in industrial education. The guide consists of a course description;…

DNA Multiple Sequence Alignment Guided by Protein Domains: The MSA-PAD 2.0 Method.

PubMed

Balech, Bachir; Monaco, Alfonso; Perniola, Michele; Santamaria, Monica; Donvito, Giacinto; Vicario, Saverio; Maggi, Giorgio; Pesole, Graziano

2018-01-01

Multiple sequence alignment (MSA) is a fundamental component in many DNA sequence analyses including metagenomics studies and phylogeny inference. When guided by protein profiles, DNA multiple alignments assume a higher precision and robustness. Here we present details of the use of the upgraded version of MSA-PAD (2.0), which is a DNA multiple sequence alignment framework able to align DNA sequences coding for single/multiple protein domains guided by PFAM or user-defined annotations. MSA-PAD has two alignment strategies, called "Gene" and "Genome," accounting for coding domains order and genomic rearrangements, respectively. Novel options were added to the present version, where the MSA can be guided by protein profiles provided by the user. This allows MSA-PAD 2.0 to run faster and to add custom protein profiles sometimes not present in PFAM database according to the user's interest. MSA-PAD 2.0 is currently freely available as a Web application at https://recasgateway.cloud.ba.infn.it/ .

A Standard System to Study Vertebrate Embryos

PubMed Central

Werneburg, Ingmar

2009-01-01

Staged embryonic series are important as reference for different kinds of biological studies. I summarise problems that occur when using ‘staging tables’ of ‘model organisms’. Investigations of developmental processes in a broad scope of taxa are becoming commonplace. Beginning in the 1990s, methods were developed to quantify and analyse developmental events in a phylogenetic framework. The algorithms associated with these methods are still under development, mainly due to difficulties of using non-independent characters. Nevertheless, the principle of comparing clearly defined newly occurring morphological features in development (events) in quantifying analyses was a key innovation for comparative embryonic research. Up to date no standard was set for how to define such events in a comparative approach. As a case study I compared the external development of 23 land vertebrate species with a focus on turtles, mainly based on reference staging tables. I excluded all the characters that are only identical for a particular species or general features that were only analysed in a few species. Based on these comparisons I defined 104 developmental characters that are common either for all vertebrates (61 characters), gnathostomes (26), tetrapods (3), amniotes (7), or only for sauropsids (7). Characters concern the neural tube, somite, ear, eye, limb, maxillary and mandibular process, pharyngeal arch, eyelid or carapace development. I present an illustrated guide listing all the defined events. This guide can be used for describing developmental series of any vertebrate species or for documenting specimen variability of a particular species. The guide incorporates drawings and photographs as well as consideration of species identifying developmental features such as colouration. The simple character-code of the guide is extendable to further characters pertaining to external and internal morphological, physiological, genetic or molecular development, and also for other vertebrate groups not examined here, such as Chondrichthyes or Actinopterygii. An online database to type in developmental events for different stages and species could be a basis for further studies in comparative embryology. By documenting developmental events with the standard code, sequence heterochrony studies (i.e. Parsimov) and studies on variability can use this broad comparative data set. PMID:19521537

Cognitive Dissonance as an Instructional Tool for Understanding Chemical Representations

ERIC Educational Resources Information Center

Corradi, David; Clarebout, Geraldine; Elen, Jan

2015-01-01

Previous research on multiple external representations (MER) indicates that sequencing representations (compared with presenting them as a whole) can, in some cases, increase conceptual understanding if there is interference between internal and external representations. We tested this mechanism by sequencing different combinations of scientific…

CNN Newsroom Classroom Guides. January 1999.

ERIC Educational Resources Information Center

Cable News Network, Atlanta, GA.

CNN Newsroom is a daily 15-minute commercial-free news program specifically produced for classroom use and provided free to participating schools. These Daily Classroom Guides support broadcasts of CNN Newsroom for January 1999. Each guide contains program rundowns for that day's broadcast, discussion activities, and links to external Web sites.…

Assembling in Sequence: A Saleable Work Skill. Occupation Simulation Packet. Grades 3rd-4th.

ERIC Educational Resources Information Center

Hueston, Jean

This teacher's guide for grades 3 and 4 contains simulated work experiences for students using the isolated skill concept - assembling in sequence. Teacher instructions include objectives, evaluation, and sequence of activities. The guide contains pre-tests and post-tests with instructions and answer keys. Three pre-skill activities are suggested,…

A novel, privacy-preserving cryptographic approach for sharing sequencing data

PubMed Central

Cassa, Christopher A; Miller, Rachel A; Mandl, Kenneth D

2013-01-01

Objective DNA samples are often processed and sequenced in facilities external to the point of collection. These samples are routinely labeled with patient identifiers or pseudonyms, allowing for potential linkage to identity and private clinical information if intercepted during transmission. We present a cryptographic scheme to securely transmit externally generated sequence data which does not require any patient identifiers, public key infrastructure, or the transmission of passwords. Materials and methods This novel encryption scheme cryptographically protects participant sequence data using a shared secret key that is derived from a unique subset of an individual’s genetic sequence. This scheme requires access to a subset of an individual’s genetic sequence to acquire full access to the transmitted sequence data, which helps to prevent sample mismatch. Results We validate that the proposed encryption scheme is robust to sequencing errors, population uniqueness, and sibling disambiguation, and provides sufficient cryptographic key space. Discussion Access to a set of an individual’s genotypes and a mutually agreed cryptographic seed is needed to unlock the full sequence, which provides additional sample authentication and authorization security. We present modest fixed and marginal costs to implement this transmission architecture. Conclusions It is possible for genomics researchers who sequence participant samples externally to protect the transmission of sequence data using unique features of an individual’s genetic sequence. PMID:23125421

Mice and Men Environmental Balance, Parts Three and Four of an Integrated Science Sequence, Teacher's Guide, 1970 Edition.

ERIC Educational Resources Information Center

Portland Project Committee, OR.

This teacher's guide contains parts three and four of the four-part first year Portland Project, a three-year secondary integrated science curriculum sequence. Part three of the guide deals with topics such as the cell, reproduction, embryology, genetics, genetic diseases, genetics and change, populations, effects of density on populations,…

CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites

PubMed Central

Naito, Yuki; Hino, Kimihiro; Bono, Hidemasa; Ui-Tei, Kumiko

2015-01-01

Summary: CRISPRdirect is a simple and functional web server for selecting rational CRISPR/Cas targets from an input sequence. The CRISPR/Cas system is a promising technique for genome engineering which allows target-specific cleavage of genomic DNA guided by Cas9 nuclease in complex with a guide RNA (gRNA), that complementarily binds to a ∼20 nt targeted sequence. The target sequence requirements are twofold. First, the 5′-NGG protospacer adjacent motif (PAM) sequence must be located adjacent to the target sequence. Second, the target sequence should be specific within the entire genome in order to avoid off-target editing. CRISPRdirect enables users to easily select rational target sequences with minimized off-target sites by performing exhaustive searches against genomic sequences. The server currently incorporates the genomic sequences of human, mouse, rat, marmoset, pig, chicken, frog, zebrafish, Ciona, fruit fly, silkworm, Caenorhabditis elegans, Arabidopsis, rice, Sorghum and budding yeast. Availability: Freely available at http://crispr.dbcls.jp/. Contact: y-naito@dbcls.rois.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25414360

Students' Experience of External Studies. Student Diary Project.

ERIC Educational Resources Information Center

Parer, Michael S.

This study examined students' experiences of external study at Gippsland Institute through the method of student self-report study diaries. Questions which were addressed include: (1) Why are external students taking courses at Gippsland? (2) What do they hope to gain? (3) How do they handle particular study guides and assignment materials? (4)…

Enhanced external quantum efficiency in GaN-based vertical-type light-emitting diodes by localized surface plasmons

PubMed Central

Yao, Yung-Chi; Hwang, Jung-Min; Yang, Zu-Po; Haung, Jing-Yu; Lin, Chia-Ching; Shen, Wei-Chen; Chou, Chun-Yang; Wang, Mei-Tan; Huang, Chun-Ying; Chen, Ching-Yu; Tsai, Meng-Tsan; Lin, Tzu-Neng; Shen, Ji-Lin; Lee, Ya-Ju

2016-01-01

Enhancement of the external quantum efficiency of a GaN-based vertical-type light emitting diode (VLED) through the coupling of localized surface plasmon (LSP) resonance with the wave-guided mode light is studied. To achieve this experimentally, Ag nanoparticles (NPs), as the LSP resonant source, are drop-casted on the most top layer of waveguide channel, which is composed of hydrothermally synthesized ZnO nanorods capped on the top of GaN-based VLED. Enhanced light-output power and external quantum efficiency are observed, and the amount of enhancement remains steady with the increase of the injected currents. To understand the observations theoretically, the absorption spectra and the electric field distributions of the VLED with and without Ag NPs decorated on ZnO NRs are determined using the finite-difference time-domain (FDTD) method. The results prove that the observation of enhancement of the external quantum efficiency can be attributed to the creation of an extra escape channel for trapped light due to the coupling of the LSP with wave-guided mode light, by which the energy of wave-guided mode light can be transferred to the efficient light scattering center of the LSP. PMID:26935648

External Prior Guided Internal Prior Learning for Real-World Noisy Image Denoising

NASA Astrophysics Data System (ADS)

Xu, Jun; Zhang, Lei; Zhang, David

2018-06-01

Most of existing image denoising methods learn image priors from either external data or the noisy image itself to remove noise. However, priors learned from external data may not be adaptive to the image to be denoised, while priors learned from the given noisy image may not be accurate due to the interference of corrupted noise. Meanwhile, the noise in real-world noisy images is very complex, which is hard to be described by simple distributions such as Gaussian distribution, making real noisy image denoising a very challenging problem. We propose to exploit the information in both external data and the given noisy image, and develop an external prior guided internal prior learning method for real noisy image denoising. We first learn external priors from an independent set of clean natural images. With the aid of learned external priors, we then learn internal priors from the given noisy image to refine the prior model. The external and internal priors are formulated as a set of orthogonal dictionaries to efficiently reconstruct the desired image. Extensive experiments are performed on several real noisy image datasets. The proposed method demonstrates highly competitive denoising performance, outperforming state-of-the-art denoising methods including those designed for real noisy images.

Reviews Opera: Doctor Atomic DVD: Doctor Atomic Equipment: Digital stopclock with external trigger Book: I Cyborg Book: Flat Earth: The History of an Infamous Idea Book: Mere Thermodynamics Book: CGP revision guides Book: Hiding the Elephant: How Magicians Invented the Impossible Book: Back of the Envelope Physics Web Watch

NASA Astrophysics Data System (ADS)

2009-07-01

WE RECOMMEND Doctor Atomic The new Doctor Atomic opera provkes discussion on ethics I Cyborg The world's first human cyborg shares his life story in I Cyborg Flat Earth: The History of an Infamous Idea Flat Earth gives us a different perspective on creationism Mere Thermodynamics An introductory text on the three laws CGP revision guides This revision guide suits all courses and every pocket Hiding the Elephant: How Magicians Invented the Impossible The mystery of many illusions are solved in this book Back of the Envelope Physics This reference deserves a place on your bookshelf WORTH A LOOK Doctor Atomic The DVD doesn't do justice to the live performance Digital stopclock with external trigger Use these stopclocks when you need an external trigger WEB WATCH Webcasts reach out to an online audience

A bacterial Argonaute with noncanonical guide RNA specificity

PubMed Central

Kaya, Emine; Doxzen, Kevin W.; Knoll, Kilian R.; Wilson, Ross C.; Strutt, Steven C.; Kranzusch, Philip J.; Doudna, Jennifer A.

2016-01-01

Eukaryotic Argonaute proteins induce gene silencing by small RNA-guided recognition and cleavage of mRNA targets. Although structural similarities between human and prokaryotic Argonautes are consistent with shared mechanistic properties, sequence and structure-based alignments suggested that Argonautes encoded within CRISPR-cas [clustered regularly interspaced short palindromic repeats (CRISPR)-associated] bacterial immunity operons have divergent activities. We show here that the CRISPR-associated Marinitoga piezophila Argonaute (MpAgo) protein cleaves single-stranded target sequences using 5′-hydroxylated guide RNAs rather than the 5′-phosphorylated guides used by all known Argonautes. The 2.0-Å resolution crystal structure of an MpAgo–RNA complex reveals a guide strand binding site comprising residues that block 5′ phosphate interactions. Using structure-based sequence alignment, we were able to identify other putative MpAgo-like proteins, all of which are encoded within CRISPR-cas loci. Taken together, our data suggest the evolution of an Argonaute subclass with noncanonical specificity for a 5′-hydroxylated guide. PMID:27035975

Transportation research methods : a guide to searching for funding opportunities.

DOT National Transportation Integrated Search

2017-03-01

This project developed a training methodology focused on external funding. This hands-on training presented the basics of external funding identification, teambuilding and collaborative partners, and proposal element design. Real-time searches and tu...

Exposure to Externalizing Peers in Early Childhood: Homophily and Peer Contagion Processes.

ERIC Educational Resources Information Center

Hanish, Laura D.; Martin, Carol Lynn; Fabes, Richard A.; Leonard, Stacie; Herzog, Melissa

2005-01-01

Guided by a transactional model, we examined the predictors and effects of exposure to externalizing peers in a low-risk sample of preschoolers and kindergarteners. On the basis of daily observations of peer interactions, we calculated measures of total exposure to externalizing peers and measures of exposure to same- and other-sex externalizing…

Guide-substrate base-pairing requirement for box H/ACA RNA-guided RNA pseudouridylation.

PubMed

De Zoysa, Meemanage D; Wu, Guowei; Katz, Raviv; Yu, Yi-Tao

2018-06-05

Box H/ACA RNAs are a group of small RNAs found in abundance in eukaryotes (as well as in archaea). Although their sequences differ, eukaryotic box H/ACA RNAs all share the same unique hairpin-hinge-hairpin-tail structure. Almost all of them function as guides that primarily direct pseudouridylation of rRNAs and spliceosomal snRNAs at specific sites. Although box H/ACA RNA-guided pseudouridylation has been extensively studied, the detailed rules governing this reaction, especially those concerning the guide RNA-substrate RNA base-pairing interactions that determine the specificity and efficiency of pseudouridylation, are still not exactly clear. This is particularly relevant given that the lengths of the guide sequences involved in base-pairing vary from one box H/ACA RNA to another. Here, we carry out a detailed investigation into guide-substrate base-pairing interactions, and identify the minimum number of base-pairs (8), required for RNA-guided pseudouridylation. In addition, we find that the pseudouridylation pocket, present in each hairpin of box H/ACA RNA, exhibits flexibility in fitting slightly different substrate sequences. Our results are consistent across three independent pseudouridylation pockets tested, suggesting that our findings are generally applicable to box H/ACA RNA-guided RNA pseudouridylation. Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Health Grades K-6. Skills-Based Scope and Sequence Guide. Target Skills and Sample Assessment Methods.

ERIC Educational Resources Information Center

Williamson, Anne; Beegle, Jenny; Gilbert, Lisa; Safaii, SeAnne; Eck, Paul; Remaley, Renea; Hasselquist, Claudia; Hatch, Kathy C.; Thompson, Kay

This guide is organized around a suggested list of health skills that all students should know and be able to do at each grade level from kindergarten through grade 6. The guide will help provide parents, teachers, and students with knowledge of what is being taught in a logical scope and sequence by grade level. It is designed to help build a…

Fractional Order PIλDμ Control for Maglev Guiding System

NASA Astrophysics Data System (ADS)

Hu, Qing; Hu, Yuwei

To effectively suppress the external disturbances and parameter perturbation problem of the maglev guiding system, and improve speed and robustness, the electromagnetic guiding system is exactly linearized using state feedback method, Fractional calculus theory is introduced, the order of integer order PID control was extended to the field of fractional, then fractional order PIλDμ Controller was presented, Due to the extra two adjustable parameters compared with traditional PID controller, fractional order PIλDμ controllers were expected to show better control performance. The results of the computer simulation show that the proposed controller suppresses the external disturbances and parameter perturbation of the system effectively; the system response speed was increased; at the same time, it had flexible structure and stronger robustness.

Simplifying the Process for Finding Research Funding: A Cross-Campus Collaboration at a Large Academic Institution.

PubMed

Rosenzweig, Merle; Smith, Judith E; Curtis, Ann; Puffenberger, Amy

2016-01-01

This article describes the collaboration between the University of Michigan's M-Library and the University of Michigan Medical School's Office of Research in developing a comprehensive online guide and consultation service. The guide was designed to assist researchers in finding available funding from both internal and external sources and was based on the results of a survey distributed by the Office of Research. Because many of the respondents were unaware of internal funding programs and needed more information on resources external to the university as well, the guide included information on both possibilities in an easy-to-use format that researchers use independently without needing further instruction, although personal consultation was also offered when necessary.

"The devil's in the detail": Release of an expanded, enhanced and dynamically revised forensic STR Sequence Guide.

PubMed

Phillips, C; Gettings, K Butler; King, J L; Ballard, D; Bodner, M; Borsuk, L; Parson, W

2018-05-01

The STR sequence template file published in 2016 as part of the considerations from the DNA Commission of the International Society for Forensic Genetics on minimal STR sequence nomenclature requirements, has been comprehensively revised and audited using the latest GRCh38 genome assembly. The list of forensic STRs characterized was expanded by including supplementary autosomal, X- and Y-chromosome microsatellites in less common use for routine DNA profiling, but some likely to be adopted in future massively parallel sequencing (MPS) STR panels. We outline several aspects of sequence alignment and annotation that required care and attention to detail when comparing sequences to GRCh37 and GRCh38 assemblies, as well as the necessary matching of MPS-based allele descriptions to previously established repeat region structures described in initial sequencing studies of the less well known forensic STRs. The revised sequence guide is now available in a dynamically updated FTP format from the STRidER website with a date-stamped change log to allow users to explore their own MPS data with the most up-to-date forensic STR sequence information compiled in a simple guide. Copyright © 2018 Elsevier B.V. All rights reserved.

Sequencing Stories in Spanish and English.

ERIC Educational Resources Information Center

Steckbeck, Pamela Meza

The guide was designed for speech pathologists, bilingual teachers, and specialists in English as a second language who work with Spanish-speaking children. The guide contains twenty illustrated stories that facilitate the learning of auditory sequencing, auditory and visual memory, receptive and expressive vocabulary, and expressive language…

AED (Automated External Defibrillator) Programs: Questions and Answers

MedlinePlus

... Training CPR In Schools Training Kits RQI AHA Blended Learning & eLearning Guide AHA Instructors ECC Educational Conferences Programs ... Training CPR In Schools Training Kits RQI AHA Blended Learning & eLearning Guide AHA Instructors ECC Educational Conferences Programs ...

Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization.

PubMed

Bedbrook, Claire N; Yang, Kevin K; Rice, Austin J; Gradinaru, Viviana; Arnold, Frances H

2017-10-01

There is growing interest in studying and engineering integral membrane proteins (MPs) that play key roles in sensing and regulating cellular response to diverse external signals. A MP must be expressed, correctly inserted and folded in a lipid bilayer, and trafficked to the proper cellular location in order to function. The sequence and structural determinants of these processes are complex and highly constrained. Here we describe a predictive, machine-learning approach that captures this complexity to facilitate successful MP engineering and design. Machine learning on carefully-chosen training sequences made by structure-guided SCHEMA recombination has enabled us to accurately predict the rare sequences in a diverse library of channelrhodopsins (ChRs) that express and localize to the plasma membrane of mammalian cells. These light-gated channel proteins of microbial origin are of interest for neuroscience applications, where expression and localization to the plasma membrane is a prerequisite for function. We trained Gaussian process (GP) classification and regression models with expression and localization data from 218 ChR chimeras chosen from a 118,098-variant library designed by SCHEMA recombination of three parent ChRs. We use these GP models to identify ChRs that express and localize well and show that our models can elucidate sequence and structure elements important for these processes. We also used the predictive models to convert a naturally occurring ChR incapable of mammalian localization into one that localizes well.

Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization

PubMed Central

Rice, Austin J.; Gradinaru, Viviana; Arnold, Frances H.

2017-01-01

There is growing interest in studying and engineering integral membrane proteins (MPs) that play key roles in sensing and regulating cellular response to diverse external signals. A MP must be expressed, correctly inserted and folded in a lipid bilayer, and trafficked to the proper cellular location in order to function. The sequence and structural determinants of these processes are complex and highly constrained. Here we describe a predictive, machine-learning approach that captures this complexity to facilitate successful MP engineering and design. Machine learning on carefully-chosen training sequences made by structure-guided SCHEMA recombination has enabled us to accurately predict the rare sequences in a diverse library of channelrhodopsins (ChRs) that express and localize to the plasma membrane of mammalian cells. These light-gated channel proteins of microbial origin are of interest for neuroscience applications, where expression and localization to the plasma membrane is a prerequisite for function. We trained Gaussian process (GP) classification and regression models with expression and localization data from 218 ChR chimeras chosen from a 118,098-variant library designed by SCHEMA recombination of three parent ChRs. We use these GP models to identify ChRs that express and localize well and show that our models can elucidate sequence and structure elements important for these processes. We also used the predictive models to convert a naturally occurring ChR incapable of mammalian localization into one that localizes well. PMID:29059183

Moving Stimuli Facilitate Synchronization But Not Temporal Perception

PubMed Central

Silva, Susana; Castro, São Luís

2016-01-01

Recent studies have shown that a moving visual stimulus (e.g., a bouncing ball) facilitates synchronization compared to a static stimulus (e.g., a flashing light), and that it can even be as effective as an auditory beep. We asked a group of participants to perform different tasks with four stimulus types: beeps, siren-like sounds, visual flashes (static) and bouncing balls. First, participants performed synchronization with isochronous sequences (stimulus-guided synchronization), followed by a continuation phase in which the stimulus was internally generated (imagery-guided synchronization). Then they performed a perception task, in which they judged whether the final part of a temporal sequence was compatible with the previous beat structure (stimulus-guided perception). Similar to synchronization, an imagery-guided variant was added, in which sequences contained a gap in between (imagery-guided perception). Balls outperformed flashes and matched beeps (powerful ball effect) in stimulus-guided synchronization but not in perception (stimulus- or imagery-guided). In imagery-guided synchronization, performance accuracy decreased for beeps and balls, but not for flashes and sirens. Our findings suggest that the advantages of moving visual stimuli over static ones are grounded in action rather than perception, and they support the hypothesis that the sensorimotor coupling mechanisms for auditory (beeps) and moving visual stimuli (bouncing balls) overlap. PMID:27909419

Moving Stimuli Facilitate Synchronization But Not Temporal Perception.

PubMed

Silva, Susana; Castro, São Luís

2016-01-01

Recent studies have shown that a moving visual stimulus (e.g., a bouncing ball) facilitates synchronization compared to a static stimulus (e.g., a flashing light), and that it can even be as effective as an auditory beep. We asked a group of participants to perform different tasks with four stimulus types: beeps, siren-like sounds, visual flashes (static) and bouncing balls. First, participants performed synchronization with isochronous sequences (stimulus-guided synchronization), followed by a continuation phase in which the stimulus was internally generated (imagery-guided synchronization). Then they performed a perception task, in which they judged whether the final part of a temporal sequence was compatible with the previous beat structure (stimulus-guided perception). Similar to synchronization, an imagery-guided variant was added, in which sequences contained a gap in between (imagery-guided perception). Balls outperformed flashes and matched beeps (powerful ball effect) in stimulus-guided synchronization but not in perception (stimulus- or imagery-guided). In imagery-guided synchronization, performance accuracy decreased for beeps and balls, but not for flashes and sirens. Our findings suggest that the advantages of moving visual stimuli over static ones are grounded in action rather than perception, and they support the hypothesis that the sensorimotor coupling mechanisms for auditory (beeps) and moving visual stimuli (bouncing balls) overlap.

On Multiple Reconnection X-lines and Tripolar Perturbations of Strong Guide Magnetic Fields

NASA Astrophysics Data System (ADS)

Eriksson, S.; Lapenta, G.; Newman, D. L.; Phan, T. D.; Gosling, J. T.; Lavraud, B.; Khotyaintsev, Yu. V.; Carr, C. M.; Markidis, S.; Goldman, M. V.

2015-05-01

We report new multi-spacecraft Cluster observations of tripolar guide magnetic field perturbations at a solar wind reconnection exhaust in the presence of a guide field BM which is almost four times as strong as the reversing field BL. The novel tripolar field consists of two narrow regions of depressed BM, with an observed 7%-14% ΔBM magnitude relative to the external field, which are found adjacent to a wide region of enhanced BM within the exhaust. A stronger reversing field is associated with each BM depression. A kinetic reconnection simulation for realistic solar wind conditions and the observed strong guide field reveals that tripolar magnetic fields preferentially form across current sheets in the presence of multiple X-lines as magnetic islands approach one another and merge into fewer and larger islands. The simulated ΔBM/ΔXN over the normal width ΔXN between a BM minimum and the edge of the external region agree with the normalized values observed by Cluster. We propose that a tripolar guide field perturbation may be used to identify candidate regions containing multiple X-lines and interacting magnetic islands at individual solar wind current sheets with a strong guide field.

Best Practices for Environmental Site Management: A Practical Guide for Applying Environmental Sequence Stratigraphy to Improve Conceptual Site Models

EPA Science Inventory

Presented here is a practical guide on the application of the geologic principles of sequence stratigraphy and facies models to the characterization of stratigraphic heterogeneity at hazardous waste sites. This technology is applicable to sites underlain by clastic aquifers (int...

Getting to Know You...All about You: Preschool Orientation Manual.

ERIC Educational Resources Information Center

San Ysidro School District, CA.

Designed to guide teachers through a 20-day sequence of preschool orientation activities, the manual presents a numbered sequence of topics with related objectives and explanations, preparation and planning needs, and specific activities for children. Section I is entitled "All Around Us" and focuses on guiding preschool children and…

Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.

PubMed

Card, Daren C; Schield, Drew R; Reyes-Velasco, Jacobo; Fujita, Matthew K; Andrew, Audra L; Oyler-McCance, Sara J; Fike, Jennifer A; Tomback, Diana F; Ruggiero, Robert P; Castoe, Todd A

2014-01-01

As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (∼3.5-5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.

Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies

USGS Publications Warehouse

Card, Daren C.; Schield, Drew R.; Reyes-Velasco, Jacobo; Fujita, Matthre K.; Andrew, Audra L.; Oyler-McCance, Sara J.; Fike, Jennifer A.; Tomback, Diana F.; Ruggiero, Robert P.; Castoe, Todd A.

2014-01-01

As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (~3.5–5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.

Structure and specificity of the RNA-guided endonuclease Cas9 during DNA interrogation, target binding and cleavage

PubMed Central

Josephs, Eric A.; Kocak, D. Dewran; Fitzgibbon, Christopher J.; McMenemy, Joshua; Gersbach, Charles A.; Marszalek, Piotr E.

2015-01-01

CRISPR-associated endonuclease Cas9 cuts DNA at variable target sites designated by a Cas9-bound RNA molecule. Cas9's ability to be directed by single ‘guide RNA’ molecules to target nearly any sequence has been recently exploited for a number of emerging biological and medical applications. Therefore, understanding the nature of Cas9's off-target activity is of paramount importance for its practical use. Using atomic force microscopy (AFM), we directly resolve individual Cas9 and nuclease-inactive dCas9 proteins as they bind along engineered DNA substrates. High-resolution imaging allows us to determine their relative propensities to bind with different guide RNA variants to targeted or off-target sequences. Mapping the structural properties of Cas9 and dCas9 to their respective binding sites reveals a progressive conformational transformation at DNA sites with increasing sequence similarity to its target. With kinetic Monte Carlo (KMC) simulations, these results provide evidence of a ‘conformational gating’ mechanism driven by the interactions between the guide RNA and the 14th–17th nucleotide region of the targeted DNA, the stabilities of which we find correlate significantly with reported off-target cleavage rates. KMC simulations also reveal potential methodologies to engineer guide RNA sequences with improved specificity by considering the invasion of guide RNAs into targeted DNA duplex. PMID:26384421

A detailed examination of the LWFA in the Self-Guided Nonlinear Blowout Regime for 15-100 Joule Lasers

NASA Astrophysics Data System (ADS)

Davidson, Asher; Tableman, Adam; Yu, Peicheng; An, Weiming; Tsung, Frank; Mori, Warren; Lu, Wei; Fonseca, Ricardo

2017-10-01

We examine scaling laws for LWFA in the regime nonlinear, self-guided regime in detail using the quasi-3D version of the particle-in-cell code OSIRIS. We find that the scaling laws continue to work well when we fix the normalized laser amplitude while reducing plasma density. It is further found that the energy gain for fixed laser energy can be improved by shortening the pulse length until self-guiding almost no longer occurs and that the energy gain can be optimized by using lasers with asymmetric longitudinal profiles. We find that when optimized, a 15 J laser may yield particle energies as high as 5.3 GeV without the need of any external guiding. Detailed studies for optimizing energy gains from 30 J and 100 J lasers will also presented which indicate that energies in excess of 10 GeV can be possible in the near term without the need for external guiding. This work is supported by the NSF and DOE.

COMOC 2: Two-dimensional aerodynamics sequence, computer program user's guide

NASA Technical Reports Server (NTRS)

Manhardt, P. D.; Orzechowski, J. A.; Baker, A. J.

1977-01-01

The COMOC finite element fluid mechanics computer program system is applicable to diverse problem classes. The two dimensional aerodynamics sequence was established for solution of the potential and/or viscous and turbulent flowfields associated with subsonic flight of elementary two dimensional isolated airfoils. The sequence is constituted of three specific flowfield options in COMOC for two dimensional flows. These include the potential flow option, the boundary layer option, and the parabolic Navier-Stokes option. By sequencing through these options, it is possible to computationally construct a weak-interaction model of the aerodynamic flowfield. This report is the user's guide to operation of COMOC for the aerodynamics sequence.

Internal wire guide for GTAW welding

NASA Technical Reports Server (NTRS)

Morgan, Gene E. (Inventor); Dyer, Gerald E. (Inventor)

1989-01-01

A welding torch for gas tungsten arc welding apparatus has a filler metal wire guide positioned within the torch, and within the shielding gas nozzle. The wire guide is adjacent to the tungsten electrode and has a ceramic liner through which the wire is fed. This reduces the size of the torch and eliminates the outside clearance problems that exit with external wire guides. Additionally, since the wire is always within the shielding gas, oxidizing of the wire is eliminated.

Mesolimbic confidence signals guide perceptual learning in the absence of external feedback

PubMed Central

Guggenmos, Matthias; Wilbertz, Gregor; Hebart, Martin N; Sterzer, Philipp

2016-01-01

It is well established that learning can occur without external feedback, yet normative reinforcement learning theories have difficulties explaining such instances of learning. Here, we propose that human observers are capable of generating their own feedback signals by monitoring internal decision variables. We investigated this hypothesis in a visual perceptual learning task using fMRI and confidence reports as a measure for this monitoring process. Employing a novel computational model in which learning is guided by confidence-based reinforcement signals, we found that mesolimbic brain areas encoded both anticipation and prediction error of confidence—in remarkable similarity to previous findings for external reward-based feedback. We demonstrate that the model accounts for choice and confidence reports and show that the mesolimbic confidence prediction error modulation derived through the model predicts individual learning success. These results provide a mechanistic neurobiological explanation for learning without external feedback by augmenting reinforcement models with confidence-based feedback. DOI: http://dx.doi.org/10.7554/eLife.13388.001 PMID:27021283

Challenges in assessing college students' conception of duality: the case of infinity

NASA Astrophysics Data System (ADS)

Babarinsa-Ochiedike, Grace Olutayo

Interpreting students' views of infinity posits a challenge for researchers due to the dynamic nature of the conception. There is diversity and variation among students' process-object perceptions. The fluctuations between students' views however reveal an undeveloped duality conception. This study examined college students' conception of duality in understanding and representing infinity with the intent to design strategies that could guide researchers in categorizing students' views of infinity into different levels. Data for the study were collected from N=238 college students enrolled in Calculus sequence courses (Pre-Calculus, Calculus I through Calculus III) at one of the southwestern universities in the U.S. using self-report questionnaires and semi-structured individual task-based interviews. Data was triangulated using multiple measures analyzed by three independent experts using self-designed coding sheets to assess students' externalization of the duality conception of infinity. Results of this study reveal that college students' experiences in traditional Calculus sequence courses are not supportive of the development of duality conception. On the contrary, it strengthens the singularity perspective on fundamental ideas of mathematics such as infinity. The study also found that coding and assessing college students' conception of duality is a challenging and complex process due to the dynamic nature of the conception that is task-dependent and context-dependent. Practical significance of the study is that it helps to recognize misconceptions and starts addressing them so students will have a more comprehensive view of fundamental mathematical ideas as they progress through the Calculus coursework sequence. The developed duality concept development framework called Action-Process-Object-Duality (APOD) adapted from the APOS theory could guide educators and researchers as they engage in assessing students' conception of duality. The results of this study could serve as a facilitating instrument to further analyze cognitive obstacles in college students' understanding of the infinity concept.

GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases.

PubMed

Zhu, Lihua Julie; Lawrence, Michael; Gupta, Ankit; Pagès, Hervé; Kucukural, Alper; Garber, Manuel; Wolfe, Scot A

2017-05-15

Genome editing technologies developed around the CRISPR-Cas9 nuclease system have facilitated the investigation of a broad range of biological questions. These nucleases also hold tremendous promise for treating a variety of genetic disorders. In the context of their therapeutic application, it is important to identify the spectrum of genomic sequences that are cleaved by a candidate nuclease when programmed with a particular guide RNA, as well as the cleavage efficiency of these sites. Powerful new experimental approaches, such as GUIDE-seq, facilitate the sensitive, unbiased genome-wide detection of nuclease cleavage sites within the genome. Flexible bioinformatics analysis tools for processing GUIDE-seq data are needed. Here, we describe an open source, open development software suite, GUIDEseq, for GUIDE-seq data analysis and annotation as a Bioconductor package in R. The GUIDEseq package provides a flexible platform with more than 60 adjustable parameters for the analysis of datasets associated with custom nuclease applications. These parameters allow data analysis to be tailored to different nuclease platforms with different length and complexity in their guide and PAM recognition sequences or their DNA cleavage position. They also enable users to customize sequence aggregation criteria, and vary peak calling thresholds that can influence the number of potential off-target sites recovered. GUIDEseq also annotates potential off-target sites that overlap with genes based on genome annotation information, as these may be the most important off-target sites for further characterization. In addition, GUIDEseq enables the comparison and visualization of off-target site overlap between different datasets for a rapid comparison of different nuclease configurations or experimental conditions. For each identified off-target, the GUIDEseq package outputs mapped GUIDE-Seq read count as well as cleavage score from a user specified off-target cleavage score prediction algorithm permitting the identification of genomic sequences with unexpected cleavage activity. The GUIDEseq package enables analysis of GUIDE-data from various nuclease platforms for any species with a defined genomic sequence. This software package has been used successfully to analyze several GUIDE-seq datasets. The software, source code and documentation are freely available at http://www.bioconductor.org/packages/release/bioc/html/GUIDEseq.html .

Teaching/Learning Guide: Level I.

ERIC Educational Resources Information Center

Carbon - Lehigh Intermediate Unit, Schnecksville, PA.

The manual presents sequences of skills designed for use as guides to teaching/learning objectives and as a basis for evaluating and recording special education students' progress. It is explained that the goal of the first level of objectives (sequenced in this document) is to enable the student to function at a motor/psychomotor state of…

Self-guided management of exome and whole-genome sequencing results: changing the results return model.

PubMed

Yu, Joon-Ho; Jamal, Seema M; Tabor, Holly K; Bamshad, Michael J

2013-09-01

Researchers and clinicians face the practical and ethical challenge of if and how to offer for return the wide and varied scope of results available from individual exome sequencing and whole-genome sequencing. We argue that rather than viewing individual exome sequencing and whole-genome sequencing as a test for which results need to be "returned," that the technology should instead be framed as a dynamic resource of information from which results should be "managed" over the lifetime of an individual. We further suggest that individual exome sequencing and whole-genome sequencing results management is optimized using a self-guided approach that enables individuals to self-select among results offered for return in a convenient, confidential, personalized context that is responsive to their value system. This approach respects autonomy, allows individuals to maximize potential benefits of genomic information (beneficence) and minimize potential harms (nonmaleficence), and also preserves their right to an open future to the extent they desire or think is appropriate. We describe key challenges and advantages of such a self-guided management system and offer guidance on implementation using an information systems approach.

User Guide to the PDS Dataset for the Cassini Composite Infrared Spectrometer (CIRS)

NASA Technical Reports Server (NTRS)

Nixon, Conor A.; Kaelberer, Monte S.; Gorius, Nicolas

2012-01-01

This User Guide to the Cassini Composite Infrared Spectrometer (CIRS) has been written with two communities in mind. First and foremost, scientists external to the Cassini Project who seek to use the CIRS data as archived in the Planetary Data System (PDS). In addition, it is intended to be a comprehensive reference guide for those internal to the CIRS team.

Directing folding pathways for multi-component DNA origami nanostructures with complex topology

NASA Astrophysics Data System (ADS)

Marras, A. E.; Zhou, L.; Kolliopoulos, V.; Su, H.-J.; Castro, C. E.

2016-05-01

Molecular self-assembly has become a well-established technique to design complex nanostructures and hierarchical mesoscale assemblies. The typical approach is to design binding complementarity into nucleotide or amino acid sequences to achieve the desired final geometry. However, with an increasing interest in dynamic nanodevices, the need to design structures with motion has necessitated the development of multi-component structures. While this has been achieved through hierarchical assembly of similar structural units, here we focus on the assembly of topologically complex structures, specifically with concentric components, where post-folding assembly is not feasible. We exploit the ability to direct folding pathways to program the sequence of assembly and present a novel approach of designing the strand topology of intermediate folding states to program the topology of the final structure, in this case a DNA origami slider structure that functions much like a piston-cylinder assembly in an engine. The ability to program the sequence and control orientation and topology of multi-component DNA origami nanostructures provides a foundation for a new class of structures with internal and external moving parts and complex scaffold topology. Furthermore, this work provides critical insight to guide the design of intermediate states along a DNA origami folding pathway and to further understand the details of DNA origami self-assembly to more broadly control folding states and landscapes.

Improper trunk rotation sequence is associated with increased maximal shoulder external rotation angle and shoulder joint force in high school baseball pitchers.

PubMed

Oyama, Sakiko; Yu, Bing; Blackburn, J Troy; Padua, Darin A; Li, Li; Myers, Joseph B

2014-09-01

In a properly coordinated throwing motion, peak pelvic rotation velocity is reached before peak upper torso rotation velocity, so that angular momentum can be transferred effectively from the proximal (pelvis) to distal (upper torso) segment. However, the effects of trunk rotation sequence on pitching biomechanics and performance have not been investigated. The aim of this study was to investigate the effects of trunk rotation sequence on ball speed and on upper extremity biomechanics that are linked to injuries in high school baseball pitchers. The hypothesis was that pitchers with improper trunk rotation sequence would demonstrate lower ball velocity and greater stress to the joint. Descriptive laboratory study. Three-dimensional pitching kinematics data were captured from 72 high school pitchers. Subjects were considered to have proper or improper trunk rotation sequences when the peak pelvic rotation velocity was reached either before or after the peak upper torso rotation velocity beyond the margin of error (±3.7% of the time from stride-foot contact to ball release). Maximal shoulder external rotation angle, elbow extension angle at ball release, peak shoulder proximal force, shoulder internal rotation moment, and elbow varus moment were compared between groups using independent t tests (α < 0.05). Pitchers with improper trunk rotation sequences (n = 33) demonstrated greater maximal shoulder external rotation angle (mean difference, 7.2° ± 2.9°, P = .016) and greater shoulder proximal force (mean difference, 9.2% ± 3.9% body weight, P = .021) compared with those with proper trunk rotation sequences (n = 22). No other variables differed significantly different between groups. High school baseball pitchers who demonstrated improper trunk rotation sequences demonstrated greater maximal shoulder external rotation angle and shoulder proximal force compared with pitchers with proper trunk rotation sequences. Improper sequencing of the trunk and torso alter upper extremity joint loading in ways that may influence injury risk. As such, exercises that reinforce the use of a proper trunk rotation sequence during the pitching motion may reduce the stress placed on the structures around the shoulder joint and lead to the prevention of injuries. © 2014 The Author(s).

Aerial Refueling Clearance Process Guide

DTIC Science & Technology

2014-08-21

using multinational/bi-lateral agreements such as the ATARES Agreement, cross servicing agreements, replacement in kind agreements, Foreign Military...Lighting 8.7.8 External Paint Scheme 8.8 External Weapons/Drop Tanks 9.0 Physical /Aerodynamic Influences 9.1 Boom Clear Path To Receptacle dhkARSAG DOC...Cold Nose Sw. 8.5 External Fuel Tanks 9.0 Physical /Aerodynamic Influence R. 9.1 Probe Clear Path ie: Obstructions, Instruments etc. 9.2 Drogue Hookup

Habits: bridging the gap between personhood and personal identity

PubMed Central

Wagner, Nils-Frederic; Northoff, Georg

2014-01-01

In philosophy, the criteria for personhood (PH) at a specific point in time (synchronic), and the necessary and sufficient conditions of personal identity (PI) over time (diachronic) are traditionally separated. Hence, the transition between both timescales of a person's life remains largely unclear. Personal habits reflect a decision-making (DM) process that binds together synchronic and diachronic timescales. Despite the fact that the actualization of habits takes place synchronically, they presuppose, for the possibility of their generation, time in a diachronic sense. The acquisition of habits therefore rests upon PI over time; that is, the temporal extension of personal decisions is the necessary condition for the possible development of habits. Conceptually, habits can thus be seen as a bridge between synchronic and diachronic timescales of a person's life. In order to investigate the empirical mediation of this temporal linkage, we draw upon the neuronal mechanisms underlying DM; in particular on the distinction between internally and externally guided DM. Externally guided DM relies on external criteria at a specific point in time (synchronic); on a neural level, this has been associated with lateral frontal and parietal brain regions. In contrast, internally guided DM is based on the person's own preferences that involve a more longitudinal and thus diachronic timescale, which has been associated with the brain's intrinsic activity. Habits can be considered to reflect a balance between internally and externally guided DM, which implicates a particular temporal balance between diachronic and synchronic elements, thus linking two different timescales. Based on such evidence, we suggest a habit-based neurophilosophical approach of PH and PI by focusing on the empirically-based linkage between the synchronic and diachronic elements of habits. By doing so, we propose to link together what philosophically has been described and analyzed separately as PH and PI. PMID:24904370

Guiding principles for peptide nanotechnology through directed discovery.

PubMed

Lampel, A; Ulijn, R V; Tuttle, T

2018-05-21

Life's diverse molecular functions are largely based on only a small number of highly conserved building blocks - the twenty canonical amino acids. These building blocks are chemically simple, but when they are organized in three-dimensional structures of tremendous complexity, new properties emerge. This review explores recent efforts in the directed discovery of functional nanoscale systems and materials based on these same amino acids, but that are not guided by copying or editing biological systems. The review summarises insights obtained using three complementary approaches of searching the sequence space to explore sequence-structure relationships for assembly, reactivity and complexation, namely: (i) strategic editing of short peptide sequences; (ii) computational approaches to predicting and comparing assembly behaviours; (iii) dynamic peptide libraries that explore the free energy landscape. These approaches give rise to guiding principles on controlling order/disorder, complexation and reactivity by peptide sequence design.

Explosion/Blast Dynamics for Constellation Launch Vehicles Assessment

NASA Technical Reports Server (NTRS)

Baer, Mel; Crawford, Dave; Hickox, Charles; Kipp, Marlin; Hertel, Gene; Morgan, Hal; Ratzel, Arthur; Cragg, Clinton H.

2009-01-01

An assessment methodology is developed to guide quantitative predictions of adverse physical environments and the subsequent effects on the Ares-1 crew launch vehicle associated with the loss of containment of cryogenic liquid propellants from the upper stage during ascent. Development of the methodology is led by a team at Sandia National Laboratories (SNL) with guidance and support from a number of National Aeronautics and Space Administration (NASA) personnel. The methodology is based on the current Ares-1 design and feasible accident scenarios. These scenarios address containment failure from debris impact or structural response to pressure or blast loading from an external source. Once containment is breached, the envisioned assessment methodology includes predictions for the sequence of physical processes stemming from cryogenic tank failure. The investigative techniques, analysis paths, and numerical simulations that comprise the proposed methodology are summarized and appropriate simulation software is identified in this report.

Guide to the measurement of tree characteristics important to the quality classification for young hardwood trees

Treesearch

David L. Sonderman

1979-01-01

A procedure is shown for measuring external tree characteristics that are important in determining the current and future quality of young hardwood trees. This guide supplements a precious study which describes the quality classification system for young hardwood trees

Reference-guided de novo assembly approach improves genome reconstruction for related species.

PubMed

Lischer, Heidi E L; Shimizu, Kentaro K

2017-11-10

The development of next-generation sequencing has made it possible to sequence whole genomes at a relatively low cost. However, de novo genome assemblies remain challenging due to short read length, missing data, repetitive regions, polymorphisms and sequencing errors. As more and more genomes are sequenced, reference-guided assembly approaches can be used to assist the assembly process. However, previous methods mostly focused on the assembly of other genotypes within the same species. We adapted and extended a reference-guided de novo assembly approach, which enables the usage of a related reference sequence to guide the genome assembly. In order to compare and evaluate de novo and our reference-guided de novo assembly approaches, we used a simulated data set of a repetitive and heterozygotic plant genome. The extended reference-guided de novo assembly approach almost always outperforms the corresponding de novo assembly program even when a reference of a different species is used. Similar improvements can be observed in high and low coverage situations. In addition, we show that a single evaluation metric, like the widely used N50 length, is not enough to properly rate assemblies as it not always points to the best assembly evaluated with other criteria. Therefore, we used the summed z-scores of 36 different statistics to evaluate the assemblies. The combination of reference mapping and de novo assembly provides a powerful tool to improve genome reconstruction by integrating information of a related genome. Our extension of the reference-guided de novo assembly approach enables the application of this strategy not only within but also between related species. Finally, the evaluation of genome assemblies is often not straight forward, as the truth is not known. Thus one should always use a combination of evaluation metrics, which not only try to assess the continuity but also the accuracy of an assembly.

Textual Design and Student Learning.

ERIC Educational Resources Information Center

Parer, Michael S.

A study was conducted to examine the relationships of four areas of textual design factors that are relevant to external students' learning as they use their course study guides: the micro and macro textual features, the linguistics, and the instructional design elements. Twelve external students from two units at the Gippsland Institute were…

Categorizing accident sequences in the external radiotherapy for risk analysis

PubMed Central

2013-01-01

Purpose This study identifies accident sequences from the past accidents in order to help the risk analysis application to the external radiotherapy. Materials and Methods This study reviews 59 accidental cases in two retrospective safety analyses that have collected the incidents in the external radiotherapy extensively. Two accident analysis reports that accumulated past incidents are investigated to identify accident sequences including initiating events, failure of safety measures, and consequences. This study classifies the accidents by the treatments stages and sources of errors for initiating events, types of failures in the safety measures, and types of undesirable consequences and the number of affected patients. Then, the accident sequences are grouped into several categories on the basis of similarity of progression. As a result, these cases can be categorized into 14 groups of accident sequence. Results The result indicates that risk analysis needs to pay attention to not only the planning stage, but also the calibration stage that is committed prior to the main treatment process. It also shows that human error is the largest contributor to initiating events as well as to the failure of safety measures. This study also illustrates an event tree analysis for an accident sequence initiated in the calibration. Conclusion This study is expected to provide sights into the accident sequences for the prospective risk analysis through the review of experiences. PMID:23865005

Mechanism of duplex DNA destabilization by RNA-guided Cas9 nuclease during target interrogation

PubMed Central

Mekler, Vladimir; Minakhin, Leonid; Severinov, Konstantin

2017-01-01

The prokaryotic clustered regularly interspaced short palindromic repeats (CRISPR)-associated 9 (Cas9) endonuclease cleaves double-stranded DNA sequences specified by guide RNA molecules and flanked by a protospacer adjacent motif (PAM) and is widely used for genome editing in various organisms. The RNA-programmed Cas9 locates the target site by scanning genomic DNA. We sought to elucidate the mechanism of initial DNA interrogation steps that precede the pairing of target DNA with guide RNA. Using fluorometric and biochemical assays, we studied Cas9/guide RNA complexes with model DNA substrates that mimicked early intermediates on the pathway to the final Cas9/guide RNA–DNA complex. The results show that Cas9/guide RNA binding to PAM favors separation of a few PAM-proximal protospacer base pairs allowing initial target interrogation by guide RNA. The duplex destabilization is mediated, in part, by Cas9/guide RNA affinity for unpaired segments of nontarget strand DNA close to PAM. Furthermore, our data indicate that the entry of double-stranded DNA beyond a short threshold distance from PAM into the Cas9/single-guide RNA (sgRNA) interior is hindered. We suggest that the interactions unfavorable for duplex DNA binding promote DNA bending in the PAM-proximal region during early steps of Cas9/guide RNA–DNA complex formation, thus additionally destabilizing the protospacer duplex. The mechanism that emerges from our analysis explains how the Cas9/sgRNA complex is able to locate the correct target sequence efficiently while interrogating numerous nontarget sequences associated with correct PAMs. PMID:28484024

Mechanism of duplex DNA destabilization by RNA-guided Cas9 nuclease during target interrogation.

PubMed

Mekler, Vladimir; Minakhin, Leonid; Severinov, Konstantin

2017-05-23

The prokaryotic clustered regularly interspaced short palindromic repeats (CRISPR)-associated 9 (Cas9) endonuclease cleaves double-stranded DNA sequences specified by guide RNA molecules and flanked by a protospacer adjacent motif (PAM) and is widely used for genome editing in various organisms. The RNA-programmed Cas9 locates the target site by scanning genomic DNA. We sought to elucidate the mechanism of initial DNA interrogation steps that precede the pairing of target DNA with guide RNA. Using fluorometric and biochemical assays, we studied Cas9/guide RNA complexes with model DNA substrates that mimicked early intermediates on the pathway to the final Cas9/guide RNA-DNA complex. The results show that Cas9/guide RNA binding to PAM favors separation of a few PAM-proximal protospacer base pairs allowing initial target interrogation by guide RNA. The duplex destabilization is mediated, in part, by Cas9/guide RNA affinity for unpaired segments of nontarget strand DNA close to PAM. Furthermore, our data indicate that the entry of double-stranded DNA beyond a short threshold distance from PAM into the Cas9/single-guide RNA (sgRNA) interior is hindered. We suggest that the interactions unfavorable for duplex DNA binding promote DNA bending in the PAM-proximal region during early steps of Cas9/guide RNA-DNA complex formation, thus additionally destabilizing the protospacer duplex. The mechanism that emerges from our analysis explains how the Cas9/sgRNA complex is able to locate the correct target sequence efficiently while interrogating numerous nontarget sequences associated with correct PAMs.

State of Iowa Scope and Sequence for Vocational Home Economics.

ERIC Educational Resources Information Center

Iowa State Dept. of Public Instruction, Des Moines. Div. of Career Education.

This scope and sequence guide for vocational home economics programs in Iowa discusses the most important dimensions of the program and describes the general purposes of programs along with factors that affect them, both in general and for Iowa specifically. The introductory chapter of the guide sets the context and the mission and also includes a…

Thermal Changes During Guided Flapless Implant Site Preparation: A Comparative Study.

PubMed

Sannino, Gianpaolo; Gherlone, Enrico F

To compare intrabony thermal changes induced by two different protocols for guided implant surgery during the whole drilling procedure. Two protocols for guided implant placement were evaluated in vitro using artificial bone cylinders. The control protocol provided traditional metal sleeves and a standard drilling sequence composed of four cylindrical triflute drills (cutting surface length = 16 mm). The test protocol provided a three-slot polyurethane sleeve and two cylindrical drills (second drill cutting surface length = 4 mm). Forty automated intermittent and graduated osteotomies (depth = 14 mm) were performed under external irrigation. Temperatures were measured in real time by three sensors at different depths (2, 8, and 13 mm). The temperature changes generated by the final drill of each protocol during the shearing and withdrawing processes were recorded as experimental results and subjected to the Student t test. Maximum temperature increases were recorded during the process of withdrawing in both protocols. In the control group, the mean thermal changes were 10.18°C, 8.61°C, and 5.78°C at depths of 2, 8, and 13 mm, respectively. In the test group, the mean thermal changes were 1.44°C, 4.46°C, and 3.58°C at depths of 2, 8, and 13 mm, respectively. The control group revealed statistically significantly (P < .0001) higher thermal changes than the test group, both in the superficial and deeper bone areas. An appropriate irrigation system could be crucial for thermal lowering during a guided implant osteotomy mainly in the coronal and middle third of the implant site. Copious irrigation should be provided during the withdrawing process since greater thermal increases could be expected. Lower temperature increases could be achieved, reducing drill-to-bone contact, ie, cutting surface length, due to short frictional force exposure.

Two Low Coverage Bird Genomes and a Comparison of Reference-Guided versus De Novo Genome Assemblies

PubMed Central

Card, Daren C.; Schield, Drew R.; Reyes-Velasco, Jacobo; Fujita, Matthew K.; Andrew, Audra L.; Oyler-McCance, Sara J.; Fike, Jennifer A.; Tomback, Diana F.; Ruggiero, Robert P.; Castoe, Todd A.

2014-01-01

As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (∼3.5–5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies. PMID:25192061

Populations, Teacher's Guide.

ERIC Educational Resources Information Center

Conard, David; Lawson, Chester A.

This Teacher's Guide is designed for use with the Science Curriculum Improvement Study's (SCIS) unit Population. Populations is the third of a six-unit sequence of SCIS's Life Science Program for grades K-6. The Populations guide consists of activity outlines along with suggestions for guiding children's observation and manipulations of living…

Unique nucleotide sequence-guided assembly of repetitive DNA parts for synthetic biology applications

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

Torella, JP; Lienert, F; Boehm, CR

2014-08-07

Recombination-based DNA construction methods, such as Gibson assembly, have made it possible to easily and simultaneously assemble multiple DNA parts, and they hold promise for the development and optimization of metabolic pathways and functional genetic circuits. Over time, however, these pathways and circuits have become more complex, and the increasing need for standardization and insulation of genetic parts has resulted in sequence redundancies-for example, repeated terminator and insulator sequences-that complicate recombination-based assembly. We and others have recently developed DNA assembly methods, which we refer to collectively as unique nucleotide sequence (UNS)-guided assembly, in which individual DNA parts are flanked withmore » UNSs to facilitate the ordered, recombination-based assembly of repetitive sequences. Here we present a detailed protocol for UNS-guided assembly that enables researchers to convert multiple DNA parts into sequenced, correctly assembled constructs, or into high-quality combinatorial libraries in only 2-3 d. If the DNA parts must be generated from scratch, an additional 2-5 d are necessary. This protocol requires no specialized equipment and can easily be implemented by a student with experience in basic cloning techniques.« less

Unique nucleotide sequence (UNS)-guided assembly of repetitive DNA parts for synthetic biology applications

PubMed Central

Torella, Joseph P.; Lienert, Florian; Boehm, Christian R.; Chen, Jan-Hung; Way, Jeffrey C.; Silver, Pamela A.

2016-01-01

Recombination-based DNA construction methods, such as Gibson assembly, have made it possible to easily and simultaneously assemble multiple DNA parts and hold promise for the development and optimization of metabolic pathways and functional genetic circuits. Over time, however, these pathways and circuits have become more complex, and the increasing need for standardization and insulation of genetic parts has resulted in sequence redundancies — for example repeated terminator and insulator sequences — that complicate recombination-based assembly. We and others have recently developed DNA assembly methods that we refer to collectively as unique nucleotide sequence (UNS)-guided assembly, in which individual DNA parts are flanked with UNSs to facilitate the ordered, recombination-based assembly of repetitive sequences. Here we present a detailed protocol for UNS-guided assembly that enables researchers to convert multiple DNA parts into sequenced, correctly-assembled constructs, or into high-quality combinatorial libraries in only 2–3 days. If the DNA parts must be generated from scratch, an additional 2–5 days are necessary. This protocol requires no specialized equipment and can easily be implemented by a student with experience in basic cloning techniques. PMID:25101822

The role of replay and theta sequences in mediating hippocampal-prefrontal interactions for memory and cognition.

PubMed

Zielinski, Mark C; Tang, Wenbo; Jadhav, Shantanu P

2017-12-18

Sequential activity is seen in the hippocampus during multiple network patterns, prominently as replay activity during both awake and sleep sharp-wave ripples (SWRs), and as theta sequences during active exploration. Although various mnemonic and cognitive functions have been ascribed to these hippocampal sequences, evidence for these proposed functions remains primarily phenomenological. Here, we briefly review current knowledge about replay events and theta sequences in spatial memory tasks. We reason that in order to gain a mechanistic and causal understanding of how these patterns influence memory and cognitive processing, it is important to consider how these sequences influence activity in other regions, and in particular, the prefrontal cortex, which is crucial for memory-guided behavior. For spatial memory tasks, we posit that hippocampal-prefrontal interactions mediated by replay and theta sequences play complementary and overlapping roles at different stages in learning, supporting memory encoding and retrieval, deliberative decision making, planning, and guiding future actions. This framework offers testable predictions for future physiology and closed-loop feedback inactivation experiments for specifically targeting hippocampal sequences as well as coordinated prefrontal activity in different network states, with the potential to reveal their causal roles in memory-guided behavior. © 2017 Wiley Periodicals, Inc.

To Guide or Not to Guide: Issues in the Sequencing of Pedagogical Structure in Computational Model-Based Learning

ERIC Educational Resources Information Center

Jacobson, Michael J.; Kim, Beaumie; Pathak, Suneeta; Zhang, BaoHui

2015-01-01

This research explores issues related to the sequencing of structure that is provided as pedagogical guidance. A study was conducted that involved grade 10 students in Singapore as they learned concepts about electricity using four NetLogo Investigations of Electricity agent-based models. It was found that the low-to-high structure learning…

Heat, Energy, and Order, Part Two of an Integrated Science Sequence, Teacher's Guide, 1970 Edition.

ERIC Educational Resources Information Center

Portland Project Committee, OR.

This teacher's guide contains part two of the four-part first year Portland Project, a three-year secondary integrated science curriculum sequence. This part involves the student with unifying principles essential for deeper understanding of the concept of energy. Confidence in the atomic nature of matter is built by relating heat in terms of…

Students' Guided Reinvention of Definition of Limit of a Sequence with Interactive Technology

ERIC Educational Resources Information Center

Flores, Alfinio; Park, Jungeun

2016-01-01

In a course emphasizing interactive technology, 19 students, including 18 mathematics education majors, mostly in their first year, reinvented the definition of limit of a sequence while working in small cooperative groups. The class spent four sessions of 75 minutes each on a cyclical process of guided reinvention of the definition of limit of a…

Waves and Particles, The Orbital Atom, Parts One and Two of an Integrated Science Sequence, Teacher's Guide, 1973 Edition.

ERIC Educational Resources Information Center

Portland Project Committee, OR.

This teacher's guide includes parts one and two of the four-part third year Portland Project, a three-year integrated secondary science curriculum sequence. The Harvard Project Physics textbook is used for reading assignments for part one. Assignments relate to waves, light, electricity, magnetic fields, Faraday and the electrical age,…

Improving CRISPR-Cas specificity with chemical modifications in single-guide RNAs.

PubMed

Ryan, Daniel E; Taussig, David; Steinfeld, Israel; Phadnis, Smruti M; Lunstad, Benjamin D; Singh, Madhurima; Vuong, Xuan; Okochi, Kenji D; McCaffrey, Ryan; Olesiak, Magdalena; Roy, Subhadeep; Yung, Chong Wing; Curry, Bo; Sampson, Jeffrey R; Bruhn, Laurakay; Dellinger, Douglas J

2018-01-25

CRISPR systems have emerged as transformative tools for altering genomes in living cells with unprecedented ease, inspiring keen interest in increasing their specificity for perfectly matched targets. We have developed a novel approach for improving specificity by incorporating chemical modifications in guide RNAs (gRNAs) at specific sites in their DNA recognition sequence ('guide sequence') and systematically evaluating their on-target and off-target activities in biochemical DNA cleavage assays and cell-based assays. Our results show that a chemical modification (2'-O-methyl-3'-phosphonoacetate, or 'MP') incorporated at select sites in the ribose-phosphate backbone of gRNAs can dramatically reduce off-target cleavage activities while maintaining high on-target performance, as demonstrated in clinically relevant genes. These findings reveal a unique method for enhancing specificity by chemically modifying the guide sequence in gRNAs. Our approach introduces a versatile tool for augmenting the performance of CRISPR systems for research, industrial and therapeutic applications. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Increasing Student Achievement: Educators' Guide to Secondary Career & Technical Education Assessment

ERIC Educational Resources Information Center

National Occupational Competency Testing Institute, 2012

2012-01-01

This guide attempts to address an aspect of secondary CTE (Career and Technical Education) that has received little attention; the assessment literacy of educators. School leaders need to go beyond ensuring routine compliance with external and internal regulatory forces to identify ways in which CTE program teachers might better understand…

Promoting, Guiding, and Surviving Change in School Districts.

ERIC Educational Resources Information Center

Deal, Terrence E.; Nutt, Samuel C.

Compiled for school administrators who must initiate or respond to external mandate for change, this guide draws on the experiences of 10 rural school districts that participated in the federally funded Experimental Schools (ES) program for perspectives that can be used in the successful management of change efforts in school districts. Organized…

Ethnicity and Health: Mexican Americans. A Guide for Health Care Providers.

ERIC Educational Resources Information Center

Roberts, Robert E.

Several characteristics and perspectives of how Mexican Americans regard health care are presented for health care providers. Following a brief discussion of culture and health, the guide describes the traditional and modern value orientations of Hispanics and the external forces that contribute to their adoption. Four key concepts to…

The Admissions Profession: A Guide for Staff Development and Program Management.

ERIC Educational Resources Information Center

American Association of Collegiate Registrars and Admissions Officers, Washington, DC.

This guide is designed to assist in college admissions staff development and program management, but is also suggested for use in training and accrediting efforts, presentations on admissions tasks, internal or external evaluations, preparation of periodic reports, and as a self-paced workbook when preparing for the admission profession, or for…

A Guide to Pathways through the Pre-Five Quality Process.

ERIC Educational Resources Information Center

Strathclyde Regional Council, Glasgow (Scotland).

This guide describes a quality process for external and internal evaluation of the elementary school education department. The term "pathway" is used to define routes through the quality process that describe any school administrative activity in terms of the indicators and examples of good practice. There are five pathways: process…

Guide to Working with Model Providers.

ERIC Educational Resources Information Center

Walter, Katie; Hassel, Bryan C.

Often a central feature of a school's improvement efforts is the adoption of a Comprehensive School Reform (CSR) model, an externally developed research-based design for school improvement. Adopting a model is only the first step in CSR. Another important step is forging partnerships with developers of CSR models. This guide aims to help schools…

Hardwood log defect photographic database, software and user's guide

Treesearch

R. Edward Thomas

2009-01-01

Computer software and user's guide for Hardwood Log Defect Photographic Database. The database contains photographs and information on external hardwood log defects and the corresponding internal characteristics. This database allows users to search for specific defect types, sizes, and locations by tree species. For every defect, the database contains photos of...

Industrial Arts Curriculum Guide for Industrial Ceramics.

ERIC Educational Resources Information Center

Connecticut State Dept. of Education, Hartford. Div. of Vocational and Adult Education.

This curriculum guide for industrial ceramics courses is part of a series of curriculum guides for use in the industrial arts curriculum in Connecticut. The guide provides information on the scope and sequence of the industrial arts curriculum, specific guidelines for industrial arts, and program goals and objectives. The content of the industrial…

Next Generation Sequencing at the University of Chicago Genomics Core

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

Faber, Pieter

2013-04-24

The University of Chicago Genomics Core provides University of Chicago investigators (and external clients) access to State-of-the-Art genomics capabilities: next generation sequencing, Sanger sequencing / genotyping and micro-arrays (gene expression, genotyping, and methylation). The current presentation will highlight our capabilities in the area of ultra-high throughput sequencing analysis.

Clinical Actionability of Comprehensive Genomic Profiling for Management of Rare or Refractory Cancers

PubMed Central

Hirshfield, Kim M.; Tolkunov, Denis; Zhong, Hua; Ali, Siraj M.; Stein, Mark N.; Murphy, Susan; Vig, Hetal; Vazquez, Alexei; Glod, John; Moss, Rebecca A.; Belyi, Vladimir; Chan, Chang S.; Chen, Suzie; Goodell, Lauri; Foran, David; Yelensky, Roman; Palma, Norma A.; Sun, James X.; Miller, Vincent A.; Stephens, Philip J.; Ross, Jeffrey S.; Kaufman, Howard; Poplin, Elizabeth; Mehnert, Janice; Tan, Antoinette R.; Bertino, Joseph R.; Aisner, Joseph; DiPaola, Robert S.

2016-01-01

Background. The frequency with which targeted tumor sequencing results will lead to implemented change in care is unclear. Prospective assessment of the feasibility and limitations of using genomic sequencing is critically important. Methods. A prospective clinical study was conducted on 100 patients with diverse-histology, rare, or poor-prognosis cancers to evaluate the clinical actionability of a Clinical Laboratory Improvement Amendments (CLIA)-certified, comprehensive genomic profiling assay (FoundationOne), using formalin-fixed, paraffin-embedded tumors. The primary objectives were to assess utility, feasibility, and limitations of genomic sequencing for genomically guided therapy or other clinical purpose in the setting of a multidisciplinary molecular tumor board. Results. Of the tumors from the 92 patients with sufficient tissue, 88 (96%) had at least one genomic alteration (average 3.6, range 0–10). Commonly altered pathways included p53 (46%), RAS/RAF/MAPK (rat sarcoma; rapidly accelerated fibrosarcoma; mitogen-activated protein kinase) (45%), receptor tyrosine kinases/ligand (44%), PI3K/AKT/mTOR (phosphatidylinositol-4,5-bisphosphate 3-kinase; protein kinase B; mammalian target of rapamycin) (35%), transcription factors/regulators (31%), and cell cycle regulators (30%). Many low frequency but potentially actionable alterations were identified in diverse histologies. Use of comprehensive profiling led to implementable clinical action in 35% of tumors with genomic alterations, including genomically guided therapy, diagnostic modification, and trigger for germline genetic testing. Conclusion. Use of targeted next-generation sequencing in the setting of an institutional molecular tumor board led to implementable clinical action in more than one third of patients with rare and poor-prognosis cancers. Major barriers to implementation of genomically guided therapy were clinical status of the patient and drug access. Early and serial sequencing in the clinical course and expanded access to genomically guided early-phase clinical trials and targeted agents may increase actionability. Implications for Practice: Identification of key factors that facilitate use of genomic tumor testing results and implementation of genomically guided therapy may lead to enhanced benefit for patients with rare or difficult to treat cancers. Clinical use of a targeted next-generation sequencing assay in the setting of an institutional molecular tumor board led to implementable clinical action in over one third of patients with rare and poor prognosis cancers. The major barriers to implementation of genomically guided therapy were clinical status of the patient and drug access both on trial and off label. Approaches to increase actionability include early and serial sequencing in the clinical course and expanded access to genomically guided early phase clinical trials and targeted agents. PMID:27566247

Foot-Matics. Teacher's Guide.

ERIC Educational Resources Information Center

Frame, Laurence

This teacher's guide contains the following sections: Teacher Objectives; Student Objectives; Teacher Aide Suggestions; Objectives Overview; Scope and Sequence (K-8); Teacher's Guide; NFL Public Relations Director; NFL Team Addresses and Art (Helmet) Pages; Football Field Dimensions; Age Problems; Statistics from a Newspaper; Standings; Weight…

in silico Whole Genome Sequencer & Analyzer (iWGS): A Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies

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

Zhou, Xiaofan; Peris, David; Kominek, Jacek

The availability of genomes across the tree of life is highly biased toward vertebrates, pathogens, human disease models, and organisms with relatively small and simple genomes. Recent progress in genomics has enabled the de novo decoding of the genome of virtually any organism, greatly expanding its potential for understanding the biology and evolution of the full spectrum of biodiversity. The increasing diversity of sequencing technologies, assays, and de novo assembly algorithms have augmented the complexity of de novo genome sequencing projects in nonmodel organisms. To reduce the costs and challenges in de novo genome sequencing projects and streamline their experimentalmore » design and analysis, we developed iWGS (in silico Whole Genome Sequencer and Analyzer), an automated pipeline for guiding the choice of appropriate sequencing strategy and assembly protocols. iWGS seamlessly integrates the four key steps of a de novo genome sequencing project: data generation (through simulation), data quality control, de novo assembly, and assembly evaluation and validation. The last three steps can also be applied to the analysis of real data. iWGS is designed to enable the user to have great flexibility in testing the range of experimental designs available for genome sequencing projects, and supports all major sequencing technologies and popular assembly tools. Three case studies illustrate how iWGS can guide the design of de novo genome sequencing projects, and evaluate the performance of a wide variety of user-specified sequencing strategies and assembly protocols on genomes of differing architectures. iWGS, along with a detailed documentation, is freely available at https://github.com/zhouxiaofan1983/iWGS.« less

in silico Whole Genome Sequencer & Analyzer (iWGS): A Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies

DOE PAGES

Zhou, Xiaofan; Peris, David; Kominek, Jacek; ...

2016-09-16

The availability of genomes across the tree of life is highly biased toward vertebrates, pathogens, human disease models, and organisms with relatively small and simple genomes. Recent progress in genomics has enabled the de novo decoding of the genome of virtually any organism, greatly expanding its potential for understanding the biology and evolution of the full spectrum of biodiversity. The increasing diversity of sequencing technologies, assays, and de novo assembly algorithms have augmented the complexity of de novo genome sequencing projects in nonmodel organisms. To reduce the costs and challenges in de novo genome sequencing projects and streamline their experimentalmore » design and analysis, we developed iWGS (in silico Whole Genome Sequencer and Analyzer), an automated pipeline for guiding the choice of appropriate sequencing strategy and assembly protocols. iWGS seamlessly integrates the four key steps of a de novo genome sequencing project: data generation (through simulation), data quality control, de novo assembly, and assembly evaluation and validation. The last three steps can also be applied to the analysis of real data. iWGS is designed to enable the user to have great flexibility in testing the range of experimental designs available for genome sequencing projects, and supports all major sequencing technologies and popular assembly tools. Three case studies illustrate how iWGS can guide the design of de novo genome sequencing projects, and evaluate the performance of a wide variety of user-specified sequencing strategies and assembly protocols on genomes of differing architectures. iWGS, along with a detailed documentation, is freely available at https://github.com/zhouxiaofan1983/iWGS.« less

Motion and Energy Chemical Reactions, Parts One and Two of an Integrated Science Sequence, Teacher's Guide, 1973 Edition.

ERIC Educational Resources Information Center

Portland Project Committee, OR.

This teacher's guide is for the second year of the Portland Project, a three-year integrated secondary science curriculum sequence. The first of two parts in this volume, "Motion and Energy," begins with the study of motion, going from the quantitative description to a consideration of what causes motion and a discussion of Newton's…

Discovering [superscript 13]C NMR, [superscript 1]H NMR, and IR Spectroscopy in the General Chemistry Laboratory through a Sequence of Guided-Inquiry Exercises

ERIC Educational Resources Information Center

Iler, H. Darrell; Justice, David; Brauer, Shari; Landis, Amanda

2012-01-01

This sequence of three guided-inquiry labs is designed for a second-semester general chemistry course and challenges students to discover basic theoretical principles associated with [superscript 13]C NMR, [superscript 1]H NMR, and IR spectroscopy. Students learn to identify and explain basic concepts of magnetic resonance and vibrational…

Chemistry of Living Matter, Energy Capture & Growth, Parts Three & Four of an Integrated Science Sequence, Teacher's Guide, 1973 Edition.

ERIC Educational Resources Information Center

Portland Project Committee, OR.

This teacher's guide includes parts three and four of the four-part third year Portland Project, a three-year integrated secondary science curriculum sequence. The underlying intention of the third year is to study energy and its importance to life. Energy-related concepts considered in year one and two, and the concepts related to atomic…

Reference-guided assembly of four diverse Arabidopsis thaliana genomes

PubMed Central

Schneeberger, Korbinian; Ossowski, Stephan; Ott, Felix; Klein, Juliane D.; Wang, Xi; Lanz, Christa; Smith, Lisa M.; Cao, Jun; Fitz, Joffrey; Warthmann, Norman; Henz, Stefan R.; Huson, Daniel H.; Weigel, Detlef

2011-01-01

We present whole-genome assemblies of four divergent Arabidopsis thaliana strains that complement the 125-Mb reference genome sequence released a decade ago. Using a newly developed reference-guided approach, we assembled large contigs from 9 to 42 Gb of Illumina short-read data from the Landsberg erecta (Ler-1), C24, Bur-0, and Kro-0 strains, which have been sequenced as part of the 1,001 Genomes Project for this species. Using alignments against the reference sequence, we first reduced the complexity of the de novo assembly and later integrated reads without similarity to the reference sequence. As an example, half of the noncentromeric C24 genome was covered by scaffolds that are longer than 260 kb, with a maximum of 2.2 Mb. Moreover, over 96% of the reference genome was covered by the reference-guided assembly, compared with only 87% with a complete de novo assembly. Comparisons with 2 Mb of dideoxy sequence reveal that the per-base error rate of the reference-guided assemblies was below 1 in 10,000. Our assemblies provide a detailed, genomewide picture of large-scale differences between A. thaliana individuals, most of which are difficult to access with alignment-consensus methods only. We demonstrate their practical relevance in studying the expression differences of polymorphic genes and show how the analysis of sRNA sequencing data can lead to erroneous conclusions if aligned against the reference genome alone. Genome assemblies, raw reads, and further information are accessible through http://1001genomes.org/projects/assemblies.html. PMID:21646520

ON MULTIPLE RECONNECTION X-LINES AND TRIPOLAR PERTURBATIONS OF STRONG GUIDE MAGNETIC FIELDS

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

Eriksson, S.; Gosling, J. T.; Lapenta, G.

We report new multi-spacecraft Cluster observations of tripolar guide magnetic field perturbations at a solar wind reconnection exhaust in the presence of a guide field B{sub M} {sub  }which is almost four times as strong as the reversing field B{sub L}. The novel tripolar field consists of two narrow regions of depressed B{sub M}, with an observed 7%–14% ΔB{sub M} magnitude relative to the external field, which are found adjacent to a wide region of enhanced B{sub M} within the exhaust. A stronger reversing field is associated with each B{sub M} depression. A kinetic reconnection simulation for realistic solar windmore » conditions and the observed strong guide field reveals that tripolar magnetic fields preferentially form across current sheets in the presence of multiple X-lines as magnetic islands approach one another and merge into fewer and larger islands. The simulated ΔB{sub M}/ΔX{sub N} over the normal width ΔX{sub N} between a B{sub M} minimum and the edge of the external region agree with the normalized values observed by Cluster. We propose that a tripolar guide field perturbation may be used to identify candidate regions containing multiple X-lines and interacting magnetic islands at individual solar wind current sheets with a strong guide field.« less

A Model of Factors Determining Students' Ability to Interpret External Representations in Biochemistry

ERIC Educational Resources Information Center

Schonborn, Konrad J.; Anderson, Trevor R.

2009-01-01

The aim of this research was to develop a model of factors affecting students' ability to interpret external representations (ERs) in biochemistry. The study was qualitative in design and was guided by the modelling framework of Justi and Gilbert. Application of the process outlined by the framework, and consultation with relevant literature, led…

Use of GDNF-Releasing Nanofiber Nerve Guide Conduits for the Repair of Conus Medullaris/Cauda Equina Injury in the Nonhuman Primate

DTIC Science & Technology

2013-10-01

Electromyography (EMG) recordings of the external anal sphincter were obtained pre- operatively as baseline records. The external anal sphincter muscle was chosen...Lee U, Chang HH, Christe KL, Havton LA. Evoked voiding contractions and corresponding urethral sphincter electromyography in non-human primates differ

What's in Your Box? Promoting Self-Reflection and Analysis of External Influences on Gender Expression and Sexual Orientation Attitudes

ERIC Educational Resources Information Center

Priest, Hannah M.

2014-01-01

This lesson plan is designed to stimulate awareness and reflection on personal attitudes toward gender expression and sexual orientation. Participants are guided to identify and analyze how external influences from various socialization agents shape gender and sexual orientation norms and, consequently, personal attitudes about gender expression…

Anatomy External [Sahuarita High School Career Curriculum Project].

ERIC Educational Resources Information Center

Esser, Robert

This course entitled "Anatomy External" is concerned with the dissection of the fetal pig, and is one of a series of instructional guides prepared by the teachers for the Sahuarita High School (Arizona) Career Curriculum Project. It consists of five units of study, and 13 behavioral objectives relating to these units are stated. The topics covered…

Drafting Lab Management Guide.

ERIC Educational Resources Information Center

Ohio State Univ., Columbus. Instructional Materials Lab.

This manual was developed to guide drafting instructors and vocational supervisors in sequencing laboratory instruction and controlling the flow of work for a 2-year machine trades training program. The first part of the guide provides information on program management (program description, safety concerns, academic issues, implementation…

KSC-07pd2452

NASA Image and Video Library

2007-09-14

KENNEDY SPACE CENTER, FLA. -- Tugboats guide the Pegasus barge carrying external tank No. 125 in the Banana River after the barge's long journey around the Florida Peninsula from the Michoud Assembly Facility near New Orleans. The barge is being towed to the turn basin in the Launch Complex 39 Area where the external tank will be offloaded and moved to the Vehicle Assembly Building. The external tank will be used on space shuttle Atlantis for mission STS-122 targeted for launch on Dec. 6. Photo credit: NASA/Troy Cryder

Real-time observation of DNA target interrogation and product release by the RNA-guided endonuclease CRISPR Cpf1 (Cas12a).

PubMed

Singh, Digvijay; Mallon, John; Poddar, Anustup; Wang, Yanbo; Tippana, Ramreddy; Yang, Olivia; Bailey, Scott; Ha, Taekjip

2018-05-22

CRISPR-Cas9, which imparts adaptive immunity against foreign genomic invaders in certain prokaryotes, has been repurposed for genome-engineering applications. More recently, another RNA-guided CRISPR endonuclease called Cpf1 (also known as Cas12a) was identified and is also being repurposed. Little is known about the kinetics and mechanism of Cpf1 DNA interaction and how sequence mismatches between the DNA target and guide-RNA influence this interaction. We used single-molecule fluorescence analysis and biochemical assays to characterize DNA interrogation, cleavage, and product release by three Cpf1 orthologs. Our Cpf1 data are consistent with the DNA interrogation mechanism proposed for Cas9. They both bind any DNA in search of protospacer-adjacent motif (PAM) sequences, verify the target sequence directionally from the PAM-proximal end, and rapidly reject any targets that lack a PAM or that are poorly matched with the guide-RNA. Unlike Cas9, which requires 9 bp for stable binding and ∼16 bp for cleavage, Cpf1 requires an ∼17-bp sequence match for both stable binding and cleavage. Unlike Cas9, which does not release the DNA cleavage products, Cpf1 rapidly releases the PAM-distal cleavage product, but not the PAM-proximal product. Solution pH, reducing conditions, and 5' guanine in guide-RNA differentially affected different Cpf1 orthologs. Our findings have important implications on Cpf1-based genome engineering and manipulation applications.

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

Petruccelli, Umberto, E-mail: umberto.petruccelli@unibas.it

Many studies about the external costs generated by the transport system have been developed in the last twenty years. To standardize methodologies and assessment procedures to be used in the evaluation of the projects, some European countries recently have adopted specific guidelines that differ from each other in some aspects even sensibly. This paper presents a critical analysis of the British, Italian and German guidelines and is aimed at cataloguing the external cost types regarded and the assessment methods indicated as well as to highlight the differences of the results, in terms of applicability and reliability. The goal is tomore » contribute to a European standardization process that would lead to the drafting of guidelines suited for all EU countries. - Highlights: • The analyzed guidelines agree on the methods to evaluate costs from air pollution, greenhouse gases and accidents. • They recommend respectively: dose-resp. approach; costs to reduce/permit emissions; whole direct, indirect and social costs. • For noise, DE guide indicates defensive expenditure or SP methods; IT guide, SP method; UK guide, the hedonic prices one. • For on territory impact, DE guide regards only the barrier effect; the IT one, also the soil consumption and system effects. • British guide proposes a qualitative methodology to estimate the impact on various landscapes and environments.« less

Land-Marine Paleoseismic Integration for the Northern Cascadia Margin, USA

NASA Astrophysics Data System (ADS)

Goldfinger, C.; Galer, S.; Beeson, J. W.; Hamilton, T. S.; Black, B.; Romsos, C. G.; Nelson, C. H.; Morey, A. E.

2015-12-01

New and archive cores (N=70), bathymetric, backscatter and sub-bottom data from the Washington margin reveal patterns of Holocene sediment transport and deposition. Barkley, Nitinat, Juan de Fuca (JDF), Quillayute, Grays, Guide, and Willapa Canyons each have different post-glacial mechanisms of loading and dispersal of sediment via turbidity currents. In high-stand conditions, the northern canyons, Barkley, Nitinat, JDF, and Quillayute are mostly relict systems. The remaining canyons, Quinault, Grays, Guide, and Willapa, are recharged to varying degrees by northward transport of Columbia River derived sediment. All systems are nonetheless active conduits for turbidity currents during the Holocene. Sedimentologic and CT analyses, supported by radiocarbon ages, micropaleontology, and the Mazama Ash show that the Holocene sedimentary sequence consists of a series of sand to mud turbidites in the active portions of all systems, interbedded with hemipelagic sediment. The relict systems are finer grained, commonly not visually detected, with Holocene turbidite counts the same as recharged systems. Use of 1960's core sketches (Atwater) fails to capture the full record, as noted by Barnard (1973). Hydrodynamic models and heavy mineral distributions show that the northern canyon systems (Barkley, Nitinat, JDF, Quillayute) are independent of the southern systems, (Quinault, Guide, Grays, Willapa) during the Holocene. Best fitting flow inversions suggest turbidity currents range in height from 80-170 m, consistent with earlier work and backscatter observations. Mass balancing suggests sediment supplied to the slope canyons and abyssal channels is 4-6 times greater than supplied by recharge to the canyon heads by external sources, strongly indicating autogenic sourcing by earthquakes. Turbidite deposition off Washington is not very sensitive to either sediment supply or slope angle. Lithostratigraphic correlation and age models of Holocene turbidite sequences suggests deposition of ~ 20 Holocene turbidites in most parts of the Canyon systems, with little variation. The explanation most consistent with the data is triggering by a series of 18-20 Holocene earthquakes, in agreement temporal and lithostratigraphic linkages to new marine sites in Canada, as well and land paleoseismic data.

Machine Trades Lab Management Guide.

ERIC Educational Resources Information Center

Ohio State Univ., Columbus. Instructional Materials Lab.

This manual was developed to guide machine trades instructors and vocational supervisors in sequencing laboratory instruction and controlling the flow of work for a 2-year machine trades training program. The first part of the guide provides information on program management (program description, safety concerns, academic issues, implementation…

Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees

PubMed Central

Yamada, Kazunori D.; Tomii, Kentaro; Katoh, Kazutaka

2016-01-01

Motivation: Large multiple sequence alignments (MSAs), consisting of thousands of sequences, are becoming more and more common, due to advances in sequencing technologies. The MAFFT MSA program has several options for building large MSAs, but their performances have not been sufficiently assessed yet, because realistic benchmarking of large MSAs has been difficult. Recently, such assessments have been made possible through the HomFam and ContTest benchmark protein datasets. Along with the development of these datasets, an interesting theory was proposed: chained guide trees increase the accuracy of MSAs of structurally conserved regions. This theory challenges the basis of progressive alignment methods and needs to be examined by being compared with other known methods including computationally intensive ones. Results: We used HomFam, ContTest and OXFam (an extended version of OXBench) to evaluate several methods enabled in MAFFT: (1) a progressive method with approximate guide trees, (2) a progressive method with chained guide trees, (3) a combination of an iterative refinement method and a progressive method and (4) a less approximate progressive method that uses a rigorous guide tree and consistency score. Other programs, Clustal Omega and UPP, available for large MSAs, were also included into the comparison. The effect of method 2 (chained guide trees) was positive in ContTest but negative in HomFam and OXFam. Methods 3 and 4 increased the benchmark scores more consistently than method 2 for the three datasets, suggesting that they are safer to use. Availability and Implementation: http://mafft.cbrc.jp/alignment/software/ Contact: katoh@ifrec.osaka-u.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27378296

Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly

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

Torella, JP; Boehm, CR; Lienert, F

2013-12-28

In vitro recombination methods have enabled one-step construction of large DNA sequences from multiple parts. Although synthetic biological circuits can in principle be assembled in the same fashion, they typically contain repeated sequence elements such as standard promoters and terminators that interfere with homologous recombination. Here we use a computational approach to design synthetic, biologically inactive unique nucleotide sequences (UNSes) that facilitate accurate ordered assembly. Importantly, our designed UNSes make it possible to assemble parts with repeated terminator and insulator sequences, and thereby create insulated functional genetic circuits in bacteria and mammalian cells. Using UNS-guided assembly to construct repeating promoter-gene-terminatormore » parts, we systematically varied gene expression to optimize production of a deoxychromoviridans biosynthetic pathway in Escherichia coli. We then used this system to construct complex eukaryotic AND-logic gates for genomic integration into embryonic stem cells. Construction was performed by using a standardized series of UNS-bearing BioBrick-compatible vectors, which enable modular assembly and facilitate reuse of individual parts. UNS-guided isothermal assembly is broadly applicable to the construction and optimization of genetic circuits and particularly those requiring tight insulation, such as complex biosynthetic pathways, sensors, counters and logic gates.« less

GUIDE-Seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases

PubMed Central

Nguyen, Nhu T.; Liebers, Matthew; Topkar, Ved V.; Thapar, Vishal; Wyvekens, Nicolas; Khayter, Cyd; Iafrate, A. John; Le, Long P.; Aryee, Martin J.; Joung, J. Keith

2014-01-01

CRISPR RNA-guided nucleases (RGNs) are widely used genome-editing reagents, but methods to delineate their genome-wide off-target cleavage activities have been lacking. Here we describe an approach for global detection of DNA double-stranded breaks (DSBs) introduced by RGNs and potentially other nucleases. This method, called Genome-wide Unbiased Identification of DSBs Enabled by Sequencing (GUIDE-Seq), relies on capture of double-stranded oligodeoxynucleotides into breaks Application of GUIDE-Seq to thirteen RGNs in two human cell lines revealed wide variability in RGN off-target activities and unappreciated characteristics of off-target sequences. The majority of identified sites were not detected by existing computational methods or ChIP-Seq. GUIDE-Seq also identified RGN-independent genomic breakpoint ‘hotspots’. Finally, GUIDE-Seq revealed that truncated guide RNAs exhibit substantially reduced RGN-induced off-target DSBs. Our experiments define the most rigorous framework for genome-wide identification of RGN off-target effects to date and provide a method for evaluating the safety of these nucleases prior to clinical use. PMID:25513782

Student-Created Definitions of Sequence Convergence: A Case Study

ERIC Educational Resources Information Center

Fisher, Brian

2016-01-01

This paper describes the development of an instructional sequence designed to allow students to reinvent the definition of sequence convergence in an introductory proof course. The sequence follows a heuristic of guided reinvention that encourages students to independently create their own mathematical definitions. This case study reports on how…

Evaluation of cost-effectiveness from the funding body's point of view of ultrasound-guided central venous catheter insertion compared with the conventional technique.

PubMed

Noritomi, Danilo Teixeira; Zigaib, Rogério; Ranzani, Otavio T; Teich, Vanessa

2016-01-01

To evaluate the cost-effectiveness, from the funding body's point of view, of real-time ultrasound-guided central venous catheter insertion compared to the traditional method, which is based on the external anatomical landmark technique. A theoretical simulation based on international literature data was applied to the Brazilian context, i.e., the Unified Health System (Sistema Único de Saúde - SUS). A decision tree was constructed that showed the two central venous catheter insertion techniques: real-time ultrasonography versus external anatomical landmarks. The probabilities of failure and complications were extracted from a search on the PubMed and Embase databases, and values associated with the procedure and with complications were taken from market research and the Department of Information Technology of the Unified Health System (DATASUS). Each central venous catheter insertion alternative had a cost that could be calculated by following each of the possible paths on the decision tree. The incremental cost-effectiveness ratio was calculated by dividing the mean incremental cost of real-time ultrasound compared to the external anatomical landmark technique by the mean incremental benefit, in terms of avoided complications. When considering the incorporation of real-time ultrasound and the concomitant lower cost due to the reduced number of complications, the decision tree revealed a final mean cost for the external anatomical landmark technique of 262.27 Brazilian reals (R$) and for real-time ultrasound of R$187.94. The final incremental cost of the real-time ultrasound-guided technique was -R$74.33 per central venous catheter. The incremental cost-effectiveness ratio was -R$2,494.34 due to the pneumothorax avoided. Real-time ultrasound-guided central venous catheter insertion was associated with decreased failure and complication rates and hypothetically reduced costs from the view of the funding body, which in this case was the SUS.

Automated real-time needle-guide tracking for fast 3-T MR-guided transrectal prostate biopsy: a feasibility study.

PubMed

Zamecnik, Patrik; Schouten, Martijn G; Krafft, Axel J; Maier, Florian; Schlemmer, Heinz-Peter; Barentsz, Jelle O; Bock, Michael; Fütterer, Jurgen J

2014-12-01

To assess the feasibility of automatic needle-guide tracking by using a real-time phase-only cross correlation ( POCC phase-only cross correlation ) algorithm-based sequence for transrectal 3-T in-bore magnetic resonance (MR)-guided prostate biopsies. This study was approved by the ethics review board, and written informed consent was obtained from all patients. Eleven patients with a prostate-specific antigen level of at least 4 ng/mL (4 μg/L) and at least one transrectal ultrasonography-guided biopsy session with negative findings were enrolled. Regions suspicious for cancer were identified on 3-T multiparametric MR images. During a subsequent MR-guided biopsy, the regions suspicious for cancer were reidentified and targeted by using the POCC phase-only cross correlation -based tracking sequence. Besides testing a general technical feasibility of the biopsy procedure by using the POCC phase-only cross correlation -based tracking sequence, the procedure times were measured, and a pathologic analysis of the biopsy cores was performed. Thirty-eight core samples were obtained from 25 regions suspicious for cancer. It was technically feasible to perform the POCC phase-only cross correlation -based biopsies in all regions suspicious for cancer in each patient, with adequate biopsy samples obtained with each biopsy attempt. The median size of the region suspicious for cancer was 8 mm (range, 4-13 mm). In each region suspicious for cancer (median number per patient, two; range, 1-4), a median of one core sample per region was obtained (range, 1-3). The median time for guidance per target was 1.5 minutes (range, 0.7-5 minutes). Nineteen of 38 core biopsy samples contained cancer. This study shows that it is feasible to perform transrectal 3-T MR-guided biopsies by using a POCC phase-only cross correlation algorithm-based real-time tracking sequence. © RSNA, 2014.

snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome.

PubMed

Yang, Jian-Hua; Zhang, Xiao-Chen; Huang, Zhan-Peng; Zhou, Hui; Huang, Mian-Bo; Zhang, Shu; Chen, Yue-Qin; Qu, Liang-Hu

2006-01-01

Small nucleolar RNAs (snoRNAs) represent an abundant group of non-coding RNAs in eukaryotes. They can be divided into guide and orphan snoRNAs according to the presence or absence of antisense sequence to rRNAs or snRNAs. Current snoRNA-searching programs, which are essentially based on sequence complementarity to rRNAs or snRNAs, exist only for the screening of guide snoRNAs. In this study, we have developed an advanced computational package, snoSeeker, which includes CDseeker and ACAseeker programs, for the highly efficient and specific screening of both guide and orphan snoRNA genes in mammalian genomes. By using these programs, we have systematically scanned four human-mammal whole-genome alignment (WGA) sequences and identified 54 novel candidates including 26 orphan candidates as well as 266 known snoRNA genes. Eighteen novel snoRNAs were further experimentally confirmed with four snoRNAs exhibiting a tissue-specific or restricted expression pattern. The results of this study provide the most comprehensive listing of two families of snoRNA genes in the human genome till date.

From Fibonacci Numbers To Geometric Sequences and the Binet Formula by Way of the Golden Ratio!

ERIC Educational Resources Information Center

DiDomenico, Angelo S.

1997-01-01

Provides activities that deal with Fibonacci-like sequences and guide students' thinking as they explore mathematical induction. Investigation leads to a discovery of an interesting relation that involves all Fibonacci-like sequences. (DDR)

Social Studies Program Guide, K-3: Primary Grades.

ERIC Educational Resources Information Center

Spokane School District 81, WA.

This curriculum guide is the first of four guides which identify the scope, sequence, goals, and resources for the social studies program of the Spokane public schools. Suggested are social studies materials, resources, and activities for kindergarten and primary grade levels. Emphasizing social studies knowledge and skill development, the guide…

Industrial Arts Curriculum Guide for Automated Machining in Metals Technology.

ERIC Educational Resources Information Center

1985

This curriculum guide is designed to be used for creating programs in automated machining education in Connecticut. The first sections of the guide are introductory, explaining the importance of computer-numerically controlled machines, describing the industrial arts scope and sequence for kindergarten through adult levels, describing the…

Latin Curriculum Guide.

ERIC Educational Resources Information Center

Lee, Agnes; Stevens, Patrick

This guide delineates the scope and sequence of Latin instruction in levels 1-3 in terms of behavioral objectives. Following a review of the Bloomington, Minnesota, school philosophy and a discussion of the design of foreign language behavioral objectives on which the guide is based, the manual discusses expected terminal behavior in the level 1…

A novel coaxial Ku-band transit radiation oscillator without external guiding magnetic field

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

Ling, Junpu, E-mail: lingjunpu@163.com; Zhang, Jiande; He, Juntao

2014-02-15

A novel coaxial transit radiation oscillator without external guiding magnetic field is designed to generate high power microwave at Ku-band. By using a coaxial structure, the space-charge potential energy is suppressed significantly, that is good for enhancing efficient beam-wave interaction. In order to improve the transmission stability of the unmagnetized intense relativistic electron beam, a Pierce-like cathode is employed in the novel device. By contrast with conventional relativistic microwave generators, this kind of device has the advantages of high stability, non-guiding magnetic field, and high efficiency. Moreover, with the coaxial design, it is possible to improve the power-handing capacity bymore » increasing the radial dimension of the Ku-band device. With a 550 keV and 7.5 kA electron beam, a 1.25 GW microwave pulse at 12.08 GHz has been obtained in the simulation. The power conversion efficiency is about 30%.« less

Cost Studies in Higher Education. The AIR Professional File, No. 7, Fall 1980.

ERIC Educational Resources Information Center

Hample, Stephen R.

A guide to cost studies in higher education is presented, with emphasis directed to the response of a four-year public institution to an externally mandated cost study. Cost studies are usually requested to guide budget allocations, either from an internal campus need or from outside pressures. Although much effort has been expended by various…

Computational studies of steering nanoparticles with magnetic gradients

NASA Astrophysics Data System (ADS)

Aylak, Sultan Suleyman

Magnetic Resonance Imaging (MRI) guided nanorobotic systems that could perform diagnostic, curative, and reconstructive treatments in the human body at the cellular and subcellular level in a controllable manner have recently been proposed. The concept of a MRI-guided nanorobotic system is based on the use of a MRI scanner to induce the required external driving forces to guide magnetic nanocapsules to a specific target. However, the maximum magnetic gradient specifications of existing clinical MRI systems are not capable of driving magnetic nanocapsules against the blood flow. This thesis presents the visualization of nanoparticles inside blood vessel, Graphical User Interface (GUI) for updating file including initial parameters and demonstrating the simulation of particles and C++ code for computing magnetic forces and fluidic forces. The visualization and GUI were designed using Virtual Reality Modeling Language (VRML), MATLAB and C#. The addition of software for MRI-guided nanorobotic system provides simulation results. Preliminary simulation results demonstrate that external magnetic field causes aggregation of nanoparticles while they flow in the vessel. This is a promising result --in accordance with similar experimental results- and encourages further investigation on the nanoparticle-based self-assembly structures for use in nanorobotic drug delivery.

Brief Guide to Genomics: DNA, Genes and Genomes

MedlinePlus

... Sheets A Brief Guide to Genomics About NHGRI Research About the International HapMap Project Biological Pathways Chromosome Abnormalities Chromosomes Cloning Comparative Genomics DNA Microarray Technology DNA Sequencing Deoxyribonucleic Acid ( ...

CAD/CAM-produced surgical guides: Optimizing the treatment workflow.

PubMed

Neugebauer, J; Kistler, F; Kistler, S; Züdorf, G; Freyer, D; Ritter, L; Dreiseidler, T; Kusch, J; Zöller, J E

2011-01-01

The increased availability of devices for 3D radiological diagnosis allows the more frequent use of CAD/CAM-produced surgical guides for implant placement. The conventional workflow requires a complex logistic chain which is time-consuming and costly. In a pilot study, the workflow of directly milled surgical guides was evaluated. These surgical guides were designed based on the fusion of an optical impression and the radiological data. The clinical use showed that the surgical guides could be accurately placed on the residual dentition without tipping movements. The conventional surgical guides were used as a control for the manual check of the deviation of the implant axis. The direct transfer of the digital planning data allows the fabrication of surgical guides in an external center without the need of physical transport, which reduces the logistic effort and expense of the central fabrication of surgical guides.

Are commercial providers a viable option for clinical bacterial sequencing?

PubMed

Raven, Kathy; Blane, Beth; Churcher, Carol; Parkhill, Julian; Peacock, Sharon J

2018-04-05

Bacterial whole-genome sequencing in the clinical setting has the potential to bring major improvements to infection control and clinical practice. Sequencing instruments are not currently available in the majority of routine microbiology laboratories worldwide, but an alternative is to use external sequencing providers. To foster discussion around this we investigated whether send-out services were a viable option. Four providers offering MiSeq sequencing were selected based on cost and evaluated based on the service provided and sequence data quality. DNA was prepared from five methicillin-resistant Staphylococcus aureus (MRSA) isolates, four of which were investigated during a previously published outbreak in the UK together with a reference MRSA isolate (ST22 HO 5096 0412). Cost of sequencing per isolate ranged from £155 to £342 and turnaround times from DNA postage to arrival of sequence data ranged from 12 to 63 days. Comparison of commercially generated genomes against the original sequence data demonstrated very high concordance, with no more than one single nucleotide polymorphism (SNP) difference on core genome mapping between the original sequences and the new sequence for all four providers. Multilocus sequence type could not be assigned based on assembly for the two cheapest sequence providers due to fragmented assemblies probably caused by a lower output of sequence data per isolate. Our results indicate that external providers returned highly accurate genome data, but that improvements are required in turnaround time to make this a viable option for use in clinical practice.

NASA's New Thermal Management Systems Roadmap; Whats in it, What it Means

NASA Technical Reports Server (NTRS)

Swanson, Ted

2016-01-01

In July of 2015 NASA publically released a new set of Technology Area Roadmaps that will be used to help guide future NASA-funded technology development efforts. One of these was the Thermal Management Systems Roadmap, often identified as TA14. This Roadmap identifies the time sequencing and interdependencies of high priority, advanced thermal control technology for the next 5 to 20 years. Available funding limits the development of new technology. The Roadmaps are the first step in the process of prioritizing HQ-supported technology funding. The 2015 Roadmaps are focused on planned mission architectures and needs, as identified in the NRC-led science Decadals and HEOMD's Design Reference Missions. Additionally, the 2015 Roadmaps focus on "applied " R&D as opposed to more basic research. The NASA Mission Directorates were all closely involved in development of 2015 Roadmaps, and an extensive external review was also conducted. This talk will discuss the Technology Roadmaps in general, and then focus on the specific technologies identified for TA 14, Thermal Management Systems.

Granting Credit for College Proficiency and Regents External Degree Examinations in New York State: A Summary of Institutional Policies, 1981-82.

ERIC Educational Resources Information Center

New York State Education Dept., Albany. Bureau of Independent Study and Programs Development.

A guide is presented for students on the policies and practices of public and private New York colleges and universities in regard to granting credit, course waiver, or advanced standing to those who pass the College Proficiency Examinations (CPEs) and the Regents External Degree Examinations (REDEs). A chart indicates, for each institution and…

SU-E-J-44: A Novel Approach to Quantify Patient Setup and Target Motion for Real-Time Image-Guided Radiotherapy (IGRT)

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

Li, S; Charpentier, P; Sayler, E

2015-06-15

Purpose Isocenter shifts and rotations to correct patient setup errors and organ motion cannot remedy some shape changes of large targets. We are investigating new methods in quantification of target deformation for realtime IGRT of breast and chest wall cancer. Methods Ninety-five patients of breast or chest wall cancer were accrued in an IRB-approved clinical trial of IGRT using 3D surface images acquired at daily setup and beam-on time via an in-room camera. Shifts and rotations relating to the planned reference surface were determined using iterative-closest-point alignment. Local surface displacements and target deformation are measured via a ray-surface intersection andmore » principal component analysis (PCA) of external surface, respectively. Isocenter shift, upper-abdominal displacement, and vectors of the surface projected onto the two principal components, PC1 and PC2, were evaluated for sensitivity and accuracy in detection of target deformation. Setup errors for some deformed targets were estimated by superlatively registering target volume, inner surface, or external surface in weekly CBCT or these outlines on weekly EPI. Results Setup difference according to the inner-surface, external surface, or target volume could be 1.5 cm. Video surface-guided setup agreed with EPI results to within < 0.5 cm while CBCT results were sometimes (∼20%) different from that of EPI (>0.5 cm) due to target deformation for some large breasts and some chest walls undergoing deep-breath-hold irradiation. Square root of PC1 and PC2 is very sensitive to external surface deformation and irregular breathing. Conclusion PCA of external surfaces is quick and simple way to detect target deformation in IGRT of breast and chest wall cancer. Setup corrections based on the target volume, inner surface, and external surface could be significant different. Thus, checking of target shape changes is essential for accurate image-guided patient setup and motion tracking of large deformable targets. NIH grant for the first author as cionsultant and the last author as the PI.« less

Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes

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

Carte, Jason; Wang, Ruiying; Li, Hong

An RNA-based gene silencing pathway that protects bacteria and archaea from viruses and other genome invaders is hypothesized to arise from guide RNAs encoded by CRISPR loci and proteins encoded by the cas genes. CRISPR loci contain multiple short invader-derived sequences separated by short repeats. The presence of virus-specific sequences within CRISPR loci of prokaryotic genomes confers resistance against corresponding viruses. The CRISPR loci are transcribed as long RNAs that must be processed to smaller guide RNAs. Here we identified Pyrococcus furiosus Cas6 as a novel endoribonuclease that cleaves CRISPR RNAs within the repeat sequences to release individual invader targetingmore » RNAs. Cas6 interacts with a specific sequence motif in the 5{prime} region of the CRISPR repeat element and cleaves at a defined site within the 3{prime} region of the repeat. The 1.8 angstrom crystal structure of the enzyme reveals two ferredoxin-like folds that are also found in other RNA-binding proteins. The predicted active site of the enzyme is similar to that of tRNA splicing endonucleases, and concordantly, Cas6 activity is metal-independent. cas6 is one of the most widely distributed CRISPR-associated genes. Our findings indicate that Cas6 functions in the generation of CRISPR-derived guide RNAs in numerous bacteria and archaea.« less

Cognitive Dissonance as an Instructional Tool for Understanding Chemical Representations

NASA Astrophysics Data System (ADS)

Corradi, David; Clarebout, Geraldine; Elen, Jan

2015-10-01

Previous research on multiple external representations (MER) indicates that sequencing representations (compared with presenting them as a whole) can, in some cases, increase conceptual understanding if there is interference between internal and external representations. We tested this mechanism by sequencing different combinations of scientific and abstract chemical representations and presenting them to 133 learners with low prior knowledge of the represented domain. The results provide insight into three separate mechanisms of learning with MER. (1) A memory (number of ideas reproduced) and (2) an accuracy (correctness of these ideas) effects occur when two representations are presented in a sequence. An accuracy and a (3) redundancy (number of redundant ideas remembered) effects occur when three representations are presented in a sequence. A necessary precondition for these effects is that descriptive formats are placed before depictive formats. The identified effects are analyzed in terms of the concept of cognitive dissonance.

A Magnetic Resonance Imaging-Conditional External Cardiac Defibrillator for Resuscitation Within the Magnetic Resonance Imaging Scanner Bore.

PubMed

Schmidt, Ehud J; Watkins, Ronald D; Zviman, Menekhem M; Guttman, Michael A; Wang, Wei; Halperin, Henry A

2016-10-01

Subjects undergoing cardiac arrest within a magnetic resonance imaging (MRI) scanner are currently removed from the bore and then from the MRI suite, before the delivery of cardiopulmonary resuscitation and defibrillation, potentially increasing the risk of mortality. This precludes many higher-risk (acute ischemic and acute stroke) patients from undergoing MRI and MRI-guided intervention. An MRI-conditional cardiac defibrillator should enable scanning with defibrillation pads attached and the generator ON, enabling application of defibrillation within the seconds of MRI after a cardiac event. An MRI-conditional external defibrillator may improve patient acceptance for MRI procedures. A commercial external defibrillator was rendered 1.5 Tesla MRI-conditional by the addition of novel radiofrequency filters between the generator and commercial disposable surface pads. The radiofrequency filters reduced emission into the MRI scanner and prevented cable/surface pad heating during imaging, while preserving all the defibrillator monitoring and delivery functions. Human volunteers were imaged using high specific absorption rate sequences to validate MRI image quality and lack of heating. Swine were electrically fibrillated (n=4) and thereafter defibrillated both outside and inside the MRI bore. MRI image quality was reduced by 0.8 or 1.6 dB, with the generator in monitoring mode and operating on battery or AC power, respectively. Commercial surface pads did not create artifacts deeper than 6 mm below the skin surface. Radiofrequency heating was within US Food and Drug Administration guidelines. Defibrillation was completely successful inside and outside the MRI bore. A prototype MRI-conditional defibrillation system successfully defibrillated in the MRI without degrading the image quality or increasing the time needed for defibrillation. It can increase patient acceptance for MRI procedures. © 2016 American Heart Association, Inc.

A comprehensive list of cloned human DNA sequences

PubMed Central

Schmidtke, Jörg; Cooper, David N.

1987-01-01

A list of DNA sequences cloned from the human genome is presented. Intended as a guide to clone availability, this list includes published reports of cDNA, genomic and synthetic clones comprising gene and pseudogene sequences, uncharacterised DNA segments and repetitive DNA elements. PMID:3575113

A comprehensive list of cloned human DNA sequences

PubMed Central

Schmidtke, Jörg; Cooper, David N.

1990-01-01

A list of DNA sequences cloned from the human genome is presented. Intended as a guide to clone availability, this list includes published reports of cDNA, genomic and synthetic clones comprising gene and pseudogene sequences, uncharacterised DNA segments and repetitive DNA elements. PMID:2333227

A comprehensive list of cloned human DNA sequences

PubMed Central

Schmidtke, Jörg; Cooper, David N.

1988-01-01

A list of DNA sequences cloned from the human genome is presented. Intended as a guide to clone availability, this list includes published reports of cDNA, genomic and synthetic clones comprising gene and pseudogene sequences, uncharacterised DNA segments and repetitive DNA elements. PMID:3368330

A comprehensive list of cloned human DNA sequences

PubMed Central

Schmidtke, Jörg; Cooper, David N.

1989-01-01

A list of DNA sequences cloned from the human genome is presented. Intended as a guide to clone availability, this list includes published reports of cDNA, genomic and synthetic clones comprising gene and pseudogene sequences, uncharacterised DNA segments and repetitive DNA elements. PMID:2654889

American History Curriculum Guide: Secondary Social Studies. Bulletin 1599. Revised.

ERIC Educational Resources Information Center

Louisiana State Dept. of Education, Baton Rouge. Div. of Academic Programs.

Developed to enhance the quality of secondary school U.S. history instruction, this curriculum guide provides implementation suggestions and includes the Louisiana social studies: (1) program rationale; (2) curriculum goals; and (3) program scope and sequence. The guide is divided into sections that feature the following themes: (1) toward a new…

World Geography Curriculum Guide: Secondary Social Studies. Bulletin 1727.

ERIC Educational Resources Information Center

Nicolosi, Louis J.; And Others

This world geography curriculum guide is designed to help teachers improve the quality of secondary level geography instruction. The guide contains Louisiana's social studies curriculum goals and information about the scope and sequence of the state's social studies program. Part 1 discusses the major geographical concepts of: (1) map and globe…

The Holocaust and Genocide: A Search for Conscience. A Curriculum Guide.

ERIC Educational Resources Information Center

Flaim, Richard F., Ed.; Reynolds, Edwin W., Jr., Ed.

Designed to facilitate teacher development of a secondary unit on the Holocaust and genocide, this multidisciplinary curriculum guide provides a wide variety of classroom-tested objectives, learning activities, and materials. The guide is organized into six units which may be taught in sequence or used in part as supplementary materials: the…

Vocational Carpentry Curriculum Guide.

ERIC Educational Resources Information Center

Virginia Polytechnic Inst. and State Univ., Blacksburg. Dept. of Education.

The carpentry curriculum guide was developed as a basic guide to be used by instructors in formulating their own courses of study. The material is designed for use in vocational carpentry classes at grade levels 10, 11, and 12. Planned as a two-year sequence, it incorporates 1080 class hours of instruction and emphasizes light or residential type…

Partial DNA-guided Cas9 enables genome editing with reduced off-target activity

PubMed Central

Yin, Hao; Song, Chun-Qing; Suresh, Sneha; Kwan, Suet-Yan; Wu, Qiongqiong; Walsh, Stephen; Ding, Junmei; Bogorad, Roman L; Zhu, Lihua Julie; Wolfe, Scot A; Koteliansky, Victor; Xue, Wen; Langer, Robert; Anderson, Daniel G

2018-01-01

CRISPR–Cas9 is a versatile RNA-guided genome editing tool. Here we demonstrate that partial replacement of RNA nucleotides with DNA nucleotides in CRISPR RNA (crRNA) enables efficient gene editing in human cells. This strategy of partial DNA replacement retains on-target activity when used with both crRNA and sgRNA, as well as with multiple guide sequences. Partial DNA replacement also works for crRNA of Cpf1, another CRISPR system. We find that partial DNA replacement in the guide sequence significantly reduces off-target genome editing through focused analysis of off-target cleavage, measurement of mismatch tolerance and genome-wide profiling of off-target sites. Using the structure of the Cas9–sgRNA complex as a guide, the majority of the 3′ end of crRNA can be replaced with DNA nucleotide, and the 5 - and 3′-DNA-replaced crRNA enables efficient genome editing. Cas9 guided by a DNA–RNA chimera may provide a generalized strategy to reduce both the cost and the off-target genome editing in human cells. PMID:29377001

Translational Medicine Guide transforms drug development processes: the recent Merck experience.

PubMed

Dolgos, Hugues; Trusheim, Mark; Gross, Dietmar; Halle, Joern-Peter; Ogden, Janet; Osterwalder, Bruno; Sedman, Ewen; Rossetti, Luciano

2016-03-01

Merck is implementing a question-based Translational Medicine Guide (TxM Guide) beginning as early as lead optimization into its stage-gate drug development process. Initial experiences with the TxM Guide, which is embedded into an integrated development plan tailored to each development program, demonstrated opportunities to improve target understanding, dose setting (i.e., therapeutic index), and patient subpopulation selection with more robust and relevant early human-based evidence, and increased use of biomarkers and simulations. The TxM Guide is also helping improve organizational learning, costs, and governance. It has also shown the need for stronger external resources for validating biomarkers, demonstrating clinical utility, tracking natural disease history, and biobanking. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

DNA targeting specificity of RNA-guided Cas9 nucleases.

PubMed

Hsu, Patrick D; Scott, David A; Weinstein, Joshua A; Ran, F Ann; Konermann, Silvana; Agarwala, Vineeta; Li, Yinqing; Fine, Eli J; Wu, Xuebing; Shalem, Ophir; Cradick, Thomas J; Marraffini, Luciano A; Bao, Gang; Zhang, Feng

2013-09-01

The Streptococcus pyogenes Cas9 (SpCas9) nuclease can be efficiently targeted to genomic loci by means of single-guide RNAs (sgRNAs) to enable genome editing. Here, we characterize SpCas9 targeting specificity in human cells to inform the selection of target sites and avoid off-target effects. Our study evaluates >700 guide RNA variants and SpCas9-induced indel mutation levels at >100 predicted genomic off-target loci in 293T and 293FT cells. We find that SpCas9 tolerates mismatches between guide RNA and target DNA at different positions in a sequence-dependent manner, sensitive to the number, position and distribution of mismatches. We also show that SpCas9-mediated cleavage is unaffected by DNA methylation and that the dosage of SpCas9 and sgRNA can be titrated to minimize off-target modification. To facilitate mammalian genome engineering applications, we provide a web-based software tool to guide the selection and validation of target sequences as well as off-target analyses.

Random and externally controlled occurrences of Dansgaard-Oeschger events

NASA Astrophysics Data System (ADS)

Lohmann, Johannes; Ditlevsen, Peter D.

2018-05-01

Dansgaard-Oeschger (DO) events constitute the most pronounced mode of centennial to millennial climate variability of the last glacial period. Since their discovery, many decades of research have been devoted to understand the origin and nature of these rapid climate shifts. In recent years, a number of studies have appeared that report emergence of DO-type variability in fully coupled general circulation models via different mechanisms. These mechanisms result in the occurrence of DO events at varying degrees of regularity, ranging from periodic to random. When examining the full sequence of DO events as captured in the North Greenland Ice Core Project (NGRIP) ice core record, one can observe high irregularity in the timing of individual events at any stage within the last glacial period. In addition to the prevailing irregularity, certain properties of the DO event sequence, such as the average event frequency or the relative distribution of cold versus warm periods, appear to be changing throughout the glacial. By using statistical hypothesis tests on simple event models, we investigate whether the observed event sequence may have been generated by stationary random processes or rather was strongly modulated by external factors. We find that the sequence of DO warming events is consistent with a stationary random process, whereas dividing the event sequence into warming and cooling events leads to inconsistency with two independent event processes. As we include external forcing, we find a particularly good fit to the observed DO sequence in a model where the average residence time in warm periods are controlled by global ice volume and cold periods by boreal summer insolation.

Photographic guide to selected external defect indicators and associated internal defects in black cherry

Treesearch

Everette D. Rast; John A. Beaton; John A. Beaton

1985-01-01

To properly classify or grade logs or trees, one must be able to correctly identify defect indicators and assess the effect of the underlying defect on possible end products. This guide aids the individual in identifying the surface defect indicator and also shows the progressive stages of the defect throughout its development for black cherry. It illustrates and...

Photographic guide to selected external defect indicators and associated internal defects in black walnut

Treesearch

Everette D.Beaton John A. Rast; David L. Sonderman; David L. Sonderman

1988-01-01

To properly classify qr grade logs or trees, one must be able to correctly identify defect indicators and assess the effect of the underlying defect on possible end products. This guide aids the individual in identifying the surface defect indicator and also shows the progressive stages of the defect throughout its develqpment for black walnut. It illustrates and...

Photographic guide of selected external defect indicators and associated internal defects in white oak

Treesearch

Everette D. Rast; John A. Beaton; David L. Sonderman; David L. Sonderman

1989-01-01

To properly classify or grade logs or trees, one must be able to correctly identify defect indicators and assess the effect of the underlying defect on possible end products. This guide assists the individual in identifying the surface defect indicator and also shows the progressive stages of the defect throughout its development for white oak. It illustrates and...

Photographic guide of selected external defect indicators and associated internal defects in northern red oak

Treesearch

Everette D. Rast

1982-01-01

To properly classify or grade logs or trees, one must be able to correctly identify defect indicators and assess the effect of the underlying defect on possible end products. This guide aids the individual in identifying the surface defect indicator and also shows the progressive stages of the defect throughout its development. It illustrates and describes eight types...

Environmental Scanning for Occupational Education. A Facilitator's Guide. A Model for Environmental Scanning to Systematically Assess Future Occupational Education and Training Needs of a Michigan Community College Service Area.

ERIC Educational Resources Information Center

Kellogg Foundation, Battle Creek, MI.

This manual is designed to facilitate the planning and implementation of an environmental scanning project in Michigan's community colleges. (Environmental scanning is a systematic process for gathering and analyzing information about the external environment and relating it to an organization's internal environment.) This facilitator's guide is…

High-throughput sequencing-based analysis of endogenetic fungal communities inhabiting the Chinese Cordyceps reveals unexpectedly high fungal diversity

PubMed Central

Xia, Fei; Chen, Xin; Guo, Meng-Yuan; Bai, Xiao-Hui; Liu, Yan; Shen, Guang-Rong; Li, Yu-Ling; Lin, Juan; Zhou, Xuan-Wei

2016-01-01

Chinese Cordyceps, known in Chinese as “DongChong XiaCao”, is a parasitic complex of a fungus (Ophiocordyceps sinensis) and a caterpillar. The current study explored the endogenetic fungal communities inhabiting Chinese Cordyceps. Samples were collected from five different geographical regions of Qinghai and Tibet, and the nuclear ribosomal internal transcribed spacer-1 sequences from each sample were obtained using Illumina high-throughput sequencing. The results showed that Ascomycota was the dominant fungal phylum in Chinese Cordyceps and its soil microhabitat from different sampling regions. Among the Ascomycota, 65 genera were identified, and the abundant operational taxonomic units showed the strongest sequence similarity to Ophiocordyceps, Verticillium, Pseudallescheria, Candida and Ilyonectria Not surprisingly, the genus Ophiocordyceps was the largest among the fungal communities identified in the fruiting bodies and external mycelial cortices of Chinese Cordyceps. In addition, fungal communities in the soil microhabitats were clustered separately from the external mycelial cortices and fruiting bodies of Chinese Cordyceps from different sampling regions. There was no significant structural difference in the fungal communities between the fruiting bodies and external mycelial cortices of Chinese Cordyceps. This study revealed an unexpectedly high diversity of fungal communities inhabiting the Chinese Cordyceps and its microhabitats. PMID:27625176

Cosmetology: Scope and Sequence.

ERIC Educational Resources Information Center

Nashville - Davidson County Metropolitan Public Schools, TN.

This scope and sequence guide, developed for a cosmetology vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

Aircraft Mechanics: Scope and Sequence.

ERIC Educational Resources Information Center

Nashville - Davidson County Metropolitan Public Schools, TN.

This scope and sequence guide, developed for an aircraft mechanics vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and…

mPUMA: a computational approach to microbiota analysis by de novo assembly of operational taxonomic units based on protein-coding barcode sequences.

PubMed

Links, Matthew G; Chaban, Bonnie; Hemmingsen, Sean M; Muirhead, Kevin; Hill, Janet E

2013-08-15

Formation of operational taxonomic units (OTU) is a common approach to data aggregation in microbial ecology studies based on amplification and sequencing of individual gene targets. The de novo assembly of OTU sequences has been recently demonstrated as an alternative to widely used clustering methods, providing robust information from experimental data alone, without any reliance on an external reference database. Here we introduce mPUMA (microbial Profiling Using Metagenomic Assembly, http://mpuma.sourceforge.net), a software package for identification and analysis of protein-coding barcode sequence data. It was developed originally for Cpn60 universal target sequences (also known as GroEL or Hsp60). Using an unattended process that is independent of external reference sequences, mPUMA forms OTUs by DNA sequence assembly and is capable of tracking OTU abundance. mPUMA processes microbial profiles both in terms of the direct DNA sequence as well as in the translated amino acid sequence for protein coding barcodes. By forming OTUs and calculating abundance through an assembly approach, mPUMA is capable of generating inputs for several popular microbiota analysis tools. Using SFF data from sequencing of a synthetic community of Cpn60 sequences derived from the human vaginal microbiome, we demonstrate that mPUMA can faithfully reconstruct all expected OTU sequences and produce compositional profiles consistent with actual community structure. mPUMA enables analysis of microbial communities while empowering the discovery of novel organisms through OTU assembly.

Proficiency testing for bacterial whole genome sequencing: an end-user survey of current capabilities, requirements and priorities.

PubMed

Moran-Gilad, Jacob; Sintchenko, Vitali; Pedersen, Susanne Karlsmose; Wolfgang, William J; Pettengill, James; Strain, Errol; Hendriksen, Rene S

2015-04-03

The advent of next-generation sequencing (NGS) has revolutionised public health microbiology. Given the potential impact of NGS, it is paramount to ensure standardisation of 'wet' laboratory and bioinformatic protocols and promote comparability of methods employed by different laboratories and their outputs. Therefore, one of the ambitious goals of the Global Microbial Identifier (GMI) initiative (http://www.globalmicrobialidentifier.org/) has been to establish a mechanism for inter-laboratory NGS proficiency testing (PT). This report presents findings from the survey recently conducted by Working Group 4 among GMI members in order to ascertain NGS end-use requirements and attitudes towards NGS PT. The survey identified the high professional diversity of laboratories engaged in NGS-based public health projects and the wide range of capabilities within institutions, at a notable range of costs. The priority pathogens reported by respondents reflected the key drivers for NGS use (high burden disease and 'high profile' pathogens). The performance of and participation in PT was perceived as important by most respondents. The wide range of sequencing and bioinformatics practices reported by end-users highlights the importance of standardisation and harmonisation of NGS in public health and underpins the use of PT as a means to assuring quality. The findings of this survey will guide the design of the GMI PT program in relation to the spectrum of pathogens included, testing frequency and volume as well as technical requirements. The PT program for external quality assurance will evolve and inform the introduction of NGS into clinical and public health microbiology practice in the post-genomic era.

Loss of preload in screwed implant joints as a function of time and tightening/untightening sequences.

PubMed

Bernardes, Sérgio Rocha; da Gloria Chiarello de Mattos, Maria; Hobkirk, John; Ribeiro, Ricardo Faria

2014-01-01

The purpose of this study was to determine whether abutment screw tightening and untightening influenced loss of preload in three different implant/abutment interfaces, or on the implant body. Five custom-fabricated machined titanium implants were used, each with its respective abutment, with different connection types, retention screws, and torque values (external hexagon with titanium screw/32 Ncm, external hexagon with coated screw/32 Ncm, internal hexagon/20 Ncm and internal conical/20 and 32 Ncm). Each implant tested had two strain gauges attached and was submitted to five tightening/untightening sequences. External hexagons resulted in the lowest preload values generated in the implant cervical third (mean of 27.75 N), while the internal hexagon had the highest values (mean of 219.61 N). There was no immediate significant loss of preload after screw tightening. Tightening/untightening sequences, regardless of the implant/abutment interface design or type of screw used in the study, did not result in any significant loss of initial preload. Conical implant connections demonstrated greater structural reinforcement within the internal connections.

College Learning Anytime, Anywhere. New Ways for Anyone to Get College Credits and College Degrees by Off-Campus Study and Examinations.

ERIC Educational Resources Information Center

Nyquist, Ewald B.; And Others

Nontraditional methods of qualifying for a college degree are described in this student guide to off-campus study and examination. The three external degree institutions in the United States that offer these programs are discussed. They include: Regents External Degree Program of the University of the State of New York; Thomas A. Edison College of…

Low-Resolution Vision-at the Hub of Eye Evolution.

PubMed

Nilsson, Dan-E; Bok, Michael J

2017-11-01

Simple roles for photoreception are likely to have preceded more demanding ones such as vision. The driving force behind this evolution is the improvement and elaboration of animal behaviors using photoreceptor input. Because the basic role for all senses aimed at the external world is to guide behavior, we argue here that understanding this "behavioral drive" is essential for unraveling the evolutionary past of the senses. Photoreception serves many different types of behavior, from simple shadow responses to visual communication. Based on minimum performance requirements for different types of tasks, photoreceptors have been argued to have evolved from non-directional receptors, via directional receptors, to low-resolution vision, and finally to high-resolution vision. Through this sequence, the performance requirements on the photoreceptors have gradually changed from broad to narrow angular sensitivity, from slow to fast response, and from low to high contrast sensitivity during the evolution from simple to more advanced and demanding behaviors. New behaviors would only evolve if their sensory performance requirements to some degree overlap with the requirements of already existing behaviors. This need for sensory "performance continuity" must have determined the order by which behaviors have evolved and thus been an important factor guiding animal evolution. Naturally, new behaviors are most likely to evolve from already existing behaviors with similar neural processing needs and similar motor responses, pointing to "neural continuity" as another guiding factor in sensory evolution. Here we use these principles to derive an evolutionary tree for behaviors driven by photoreceptor input. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

K-12 Energy Education Program: A Conceptual Guide To K-12 Energy Education in Wisconsin.

ERIC Educational Resources Information Center

Wisconsin Univ., Stevens Point. Energy Center of Wisconsin.

In addition to presenting concepts that can help students understand and make decisions about energy issues, this guide provides guidance for teachers to incorporate energy education into their curricula. The guide is divided into two major sections: (1) the Energy Education Conceptual Framework and (2) the Suggested Scope and Sequence. The…

Biology--Chemistry--Physics, Students' Guide, A Three-Year Sequence, Parts I and II.

ERIC Educational Resources Information Center

Scott, Arthur; And Others

Parts I and II of the students' guide to the three-year integrated biology, chemistry, and physics course being prepared by the Portland Project Committee are contained in this guide. A committee reviewed and selected material developed by the national course improvement groups--Physical Science Study Committee, Chemical Bond Approach, Chemical…

Textile Science Leader's Guide. 4-H Textile Science.

ERIC Educational Resources Information Center

Scholl, Jan

This instructor's guide provides an overview of 4-H student project modules in the textile sciences area. The guide includes short notes explaining how to use the project modules, a flowchart chart showing how the project areas are sequenced, a synopsis of the design and content of the modules, and some program planning tips. For each of the…

Spanish Oral Language Guide: Kindergarten Level. Espanol como Segundo Idioma. Teacher's Guide: Level I.

ERIC Educational Resources Information Center

Corbell, Gloria; And Others

This teacher's guide to Spanish language at the kindergarten level includes a recommended subject presentation sequence for the Spanish curriculum, a sample schedule, a grouping of students using three stations, and a classroom layout. The grouping would be effective when at least one-third of the children are Spanish-speaking or bilingual. The…

A Guide to Business Course Competencies. The Business Program in Virginia.

ERIC Educational Resources Information Center

Henrico County Public Schools, Glen Allen, VA. Virginia Vocational Curriculum and Resource Center.

This curriculum guide was developed as a model for schools in Virginia to prepare local programs of studies in business education. The Business Program contains 21 courses plus a 4-year sequence of courses for office specialist and a local option for students with disabilities. This guide contains an overview of the Business Program, information…

Advanced Marketing 8130. Planning for Entrepreneurship. Teacher's Resource Guide.

ERIC Educational Resources Information Center

Virginia State Dept. of Education, Richmond.

This teacher's guide is designed for use in a one-semester course to provide marketing and distributive education students with the skills necessary to open a marketing business. Included in the guide are a task list, a suggested teaching sequence, and a series of nine instructional units. The following topics are addressed in the individual…

LATIN FOR SECONDARY SCHOOLS (A GUIDE TO MINIMUM ESSENTIALS).

ERIC Educational Resources Information Center

LEAMON, M. PHILLIP; AND OTHERS

A SET OF MINIMUM ESSENTIALS FOR EACH LEVEL OF A 4-YEAR SEQUENCE OF LATIN IN SECONDARY SCHOOLS IS PRESENTED IN THIS CURRICULUM GUIDE. FOLLOWING STATEMENTS OF THE OBJECTIVES OF LATIN STUDY--READING THE LATIN OF THE GREAT ROMAN AUTHORS, ATTAINING A LINGUISTIC PROFICIENCY, AND ACQUIRING A WIDER HISTORICAL AND CULTURAL AWARENESS--THE GUIDE OUTLINES FOR…

Auto Mechanics: Scope and Sequence.

ERIC Educational Resources Information Center

Nashville - Davidson County Metropolitan Public Schools, TN.

This scope and sequence guide, developed for an auto mechanics vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

Diesel Mechanics: Scope and Sequence.

ERIC Educational Resources Information Center

Nashville - Davidson County Metropolitan Public Schools, TN.

This scope and sequence guide, developed for a diesel mechanics vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

Air Conditioning, Heating, and Refrigeration: Scope and Sequence.

ERIC Educational Resources Information Center

Nashville - Davidson County Metropolitan Public Schools, TN.

This scope and sequence guide, developed for an air conditioning, heating, and refrigeration vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed…

Commercial Art: Scope and Sequence.

ERIC Educational Resources Information Center

Nashville - Davidson County Metropolitan Public Schools, TN.

This scope and sequence guide, developed for a commercial art vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

From Arithmetic Sequences to Linear Equations

ERIC Educational Resources Information Center

Matsuura, Ryota; Harless, Patrick

2012-01-01

The first part of the article focuses on deriving the essential properties of arithmetic sequences by appealing to students' sense making and reasoning. The second part describes how to guide students to translate their knowledge of arithmetic sequences into an understanding of linear equations. Ryota Matsuura originally wrote these lessons for…

RNA-programmed genome editing in human cells

PubMed Central

Jinek, Martin; East, Alexandra; Cheng, Aaron; Lin, Steven; Ma, Enbo; Doudna, Jennifer

2013-01-01

Type II CRISPR immune systems in bacteria use a dual RNA-guided DNA endonuclease, Cas9, to cleave foreign DNA at specific sites. We show here that Cas9 assembles with hybrid guide RNAs in human cells and can induce the formation of double-strand DNA breaks (DSBs) at a site complementary to the guide RNA sequence in genomic DNA. This cleavage activity requires both Cas9 and the complementary binding of the guide RNA. Experiments using extracts from transfected cells show that RNA expression and/or assembly into Cas9 is the limiting factor for Cas9-mediated DNA cleavage. In addition, we find that extension of the RNA sequence at the 3′ end enhances DNA targeting activity in vivo. These results show that RNA-programmed genome editing is a facile strategy for introducing site-specific genetic changes in human cells. DOI: http://dx.doi.org/10.7554/eLife.00471.001 PMID:23386978

EPA Communications Stylebook

EPA Pesticide Factsheets

This currently effective Stylebook developed by the Office of External Affairs and Environmental Education (OEAEE) includes a checklist for communications product development, publication and web writing guide, and graphics and logo usage and policies.

Magnetic guide-wire navigation in pulmonary and systemic arterial catheterization: initial experience in pigs.

PubMed

Grosse-Wortmann, Lars; Grabitz, Ralf; Seghaye, Marie-Christine

2007-04-01

Cardiovascular catheterization can be challenging whenever a stenosis or an abnormal vascular course interferes with probing the target vessel. This study addresses the feasibility of navigating a guide wire with a magnetic tip by an external magnetic field through pulmonary and systemic arteries in an experimental porcine model. We investigated six piglets using magnetic guide-wire navigation. Two pulmonary arteriograms were taken from different angles in order to reconstruct the three-dimensional vessel anatomy. A computer interface then calculated three-dimensional coordinates for the vessel in space. Using these coordinates, two external magnets were positioned to create magnetic vectors along the expected vessel course. Magnetically enabled guide wires were then navigated into the vessels using the magnetic field to orient the guide-wire tips. Aortic and renal branches were addressed in a similar fashion. Difficulty in reaching the target vessel was reflected by the number of attempts that were necessary. After 10 failed attempts, the maneuver was recorded to have failed. Thirty-five of 37 (94.6%) arteries with branches at acute angles were reached successfully using magnetic navigation. In two pigs, the left upper lobe artery could not be probed. Peripheral arteries of small diameter were easier to reach than large central arteries, requiring less attempts. Magnetic guide-wire navigation is feasible in the arteries of the lungs, the head and neck, and the kidneys. It is particularly useful in entering small arterial branches at acute angles and may facilitate interventional therapy in a variety of vascular diseases in children and adults.

Inverted temperature sequences: role of deformation partitioning

NASA Astrophysics Data System (ADS)

Grujic, D.; Ashley, K. T.; Coble, M. A.; Coutand, I.; Kellett, D.; Whynot, N.

2015-12-01

The inverted metamorphism associated with the Main Central thrust zone in the Himalaya has been historically attributed to a number of tectonic processes. Here we show that there is actually a composite peak and deformation temperature sequence that formed in succession via different tectonic processes. The deformation partitioning seems to the have played a key role, and the magnitude of each process has varied along strike of the orogen. To explain the formation of the inverted metamorphic sequence across the Lesser Himalayan Sequence (LHS) in eastern Bhutan, we used Raman spectroscopy of carbonaceous material (RSCM) to determine the peak metamorphic temperatures and Ti-in-quartz thermobarometry to determine the deformation temperatures combined with thermochronology including published apatite and zircon U-Th/He and fission-track data and new 40Ar/39Ar dating of muscovite. The dataset was inverted using 3D-thermal-kinematic modeling to constrain the ranges of geological parameters such as fault geometry and slip rates, location and rates of localized basal accretion, and thermal properties of the crust. RSCM results indicate that there are two peak temperature sequences separated by a major thrust within the LHS. The internal temperature sequence shows an inverted peak temperature gradient of 12 °C/km; in the external (southern) sequence, the peak temperatures are constant across the structural sequence. Thermo-kinematic modeling suggest that the thermochronologic and thermobarometric data are compatible with a two-stage scenario: an Early-Middle Miocene phase of fast overthrusting of a hot hanging wall over a downgoing footwall and inversion of the synkinematic isotherms, followed by the formation of the external duplex developed by dominant underthrusting and basal accretion. To reconcile our observations with the experimental data, we suggest that pervasive ductile deformation within the upper LHS and along the Main Central thrust zone at its top stopped at ~11 Ma at which time the deformation shifted and focused within the external duplex and the Main Boundary Thrust.

A Guide for Educators to Move beyond Conventional School Playgrounds: The RE-AIM Evaluation of the Lunchtime Enjoyment Activity and Play (LEAP) Intervention

ERIC Educational Resources Information Center

Hyndman, Brendon P; Benson, Amanda C.; Telford, Amanda

2014-01-01

Despite an increase in the provision of effective school-based interventions in recent times, there is an absence of literature for teachers focusing on the translation of promising interventions into real-world practice. The aim of this research was to provide a social-ecological guide for teachers of the external validity of implementing the…

Educable Mentally Handicapped: Curriculum Guide.

ERIC Educational Resources Information Center

Alberta Dept. of Education, Edmonton.

The curriculum guide outlines objectives, strategies, and materials for developing academic, daily living, and vocational skills in educable mentally retarded students. An introductory section explains that the curriculum incorporates a community focus, parental involvement, developmental sequencing, and prescriptive teaching. Guidelines to…

EMH Curriculum Guide.

ERIC Educational Resources Information Center

Gwinnett County Schools, GA.

The guide consists of behaviorally stated, developmentally sequenced curriculum objectives for mentally retarded students from preprimary through high school levels. Five major sections present detailed skill objectives in the following areas: (1) basic academic skills (motor development, perceptual development, language development, reading,…

Civil Engineering Technology Program Guide.

ERIC Educational Resources Information Center

Georgia Univ., Athens. Dept. of Vocational Education.

This program guide presents civil engineering technology curriculum for technical institutes in Georgia. The general information section contains the following: purpose and objectives; program description, including admissions, typical job titles, and accreditation and certification; and curriculum model, including standard curriculum sequence and…

Subsolar magnetopause observation and kinetic simulation of a tripolar guide magnetic field perturbation consistent with a magnetic island

NASA Astrophysics Data System (ADS)

Eriksson, S.; Cassak, P. A.; Retinò, A.; Mozer, F. S.

2016-04-01

The Polar satellite recorded two reconnection exhausts within 6 min on 1 April 2001 across a subsolar magnetopause that displayed a symmetric plasma density, but different out-of-plane magnetic field signatures for similar solar wind conditions. The first magnetopause crossing displayed a bipolar guide field variation in a weak external guide field consistent with a symmetric Hall field from a single X line. The subsequent crossing represents the first observation of a tripolar guide field perturbation at Earth's magnetopause in a strong guide field. This perturbation consists of a significant guide field enhancement between two narrow guide field depressions. A particle-in-cell simulation for the prevailing conditions across this second event resulted in a magnetic island between two simulated X lines across which a tripolar guide field developed consistent with the observation. The simulated island supports a scenario whereby Polar encountered the asymmetric quadrupole Hall magnetic fields between two X lines for symmetric conditions across the magnetopause.

Chimeric Rhinoviruses Displaying MPER Epitopes Elicit Anti-HIV Neutralizing Responses

PubMed Central

Yi, Guohua; Lapelosa, Mauro; Bradley, Rachel; Mariano, Thomas M.; Dietz, Denise Elsasser; Hughes, Scott; Wrin, Terri; Petropoulos, Chris; Gallicchio, Emilio; Levy, Ronald M.; Arnold, Eddy; Arnold, Gail Ferstandig

2013-01-01

Background The development of an effective AIDS vaccine has been a formidable task, but remains a critical necessity. The well conserved membrane-proximal external region (MPER) of the HIV-1 gp41 glycoprotein is one of the crucial targets for AIDS vaccine development, as it has the necessary attribute of being able to elicit antibodies capable of neutralizing diverse isolates of HIV. Methodology/Principle Findings Guided by X-ray crystallography, molecular modeling, combinatorial chemistry, and powerful selection techniques, we designed and produced six combinatorial libraries of chimeric human rhinoviruses (HRV) displaying the MPER epitopes corresponding to mAbs 2F5, 4E10, and/or Z13e1, connected to an immunogenic surface loop of HRV via linkers of varying lengths and sequences. Not all libraries led to viable chimeric viruses with the desired sequences, but the combinatorial approach allowed us to examine large numbers of MPER-displaying chimeras. Among the chimeras were five that elicited antibodies capable of significantly neutralizing HIV-1 pseudoviruses from at least three subtypes, in one case leading to neutralization of 10 pseudoviruses from all six subtypes tested. Conclusions Optimization of these chimeras or closely related chimeras could conceivably lead to useful components of an effective AIDS vaccine. While the MPER of HIV may not be immunodominant in natural infection by HIV-1, its presence in a vaccine cocktail could provide critical breadth of protection. PMID:24039745

Mice and Men Environmental Balance, Parts Three and Four of an Integrated Science Sequence, Student Guide, 1970 Edition.

ERIC Educational Resources Information Center

Portland Project Committee, OR.

This student guide is divided into two sections: "Mice and Men" and "Environmental Balance," and constitutes parts three and four of the first year of the Portland Project, a three-year, integrated high school science curriculum. Part One of the guide deals with topics such as cell, reproduction, embryology, genetics, genetic…

Building a Linked Learning Pathway: A Guide for Transforming High Schools for College and Career Success

ERIC Educational Resources Information Center

Atterbury, Rob

2014-01-01

This guide provides an overview of a more robust online guide and toolkit available through ConnectEd Studios. It supplies a glimpse of the sequence of steps involved in creating a new Linked Learning pathway. This publication can help coaches, district leadership, and pathway teams gain an understanding of the overall process of designing and…

Optimized guide RNA structure for genome editing via Cas9

PubMed Central

Xu, Jianyong; Lian, Wei; Jia, Yuning; Li, Lingyun; Huang, Zhong

2017-01-01

The genome editing tool Cas9-gRNA (guide RNA) has been successfully applied in different cell types and organisms with high efficiency. However, more efforts need to be made to enhance both efficiency and specificity. In the current study, we optimized the guide RNA structure of Streptococcus pyogenes CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas (CRISPR-associated) system to improve its genome editing efficiency. Comparing with the original functional structure of guide RNA, which is composed of crRNA and tracrRNA, the widely used chimeric gRNA has shorter crRNA and tracrRNA sequence. The deleted RNA sequence could form extra loop structure, which might enhance the stability of the guide RNA structure and subsequently the genome editing efficiency. Thus the genome editing efficiency of different forms of guide RNA was tested. And we found that the chimeric structure of gRNA with original full length of crRNA and tracrRNA showed higher genome editing efficiency than the conventional chimeric structure or other types of gRNA we tested. Therefore our data here uncovered the new type of gRNA structure with higher genome editing efficiency. PMID:29212218

Use of GDNF-Releasing Nanofiber Nerve Guide Conduits for the Repair of Conus medullaris/Cauda Equina Injury in the Non-Human Primate

DTIC Science & Technology

2011-10-01

Cauda equina, non-human primate, ventral root. neural repair, electromyography , magnetic resonance imaging 16. SECURITY CLASSIFICATION OF: 17...of a guidance channel without GDNF release and a peripheral nerve graft to bridge the tissue gap. A comprehensive set of electrodiagnostic, imaging ... Electromyography (EMG) recordings of the external anal sphincter are obtained pre-operatively as baseline records. The external anal sphincter muscle

Encoding and choice in the task span paradigm.

PubMed

Reiman, Kaitlin M; Weaver, Starla M; Arrington, Catherine M

2015-03-01

Cognitive control during sequences of planned behaviors requires both plan-level processes such as generating, maintaining, and monitoring the plan, as well as task-level processes such as selecting, establishing and implementing specific task sets. The task span paradigm (Logan in J Exp Psychol Gen 133:218-236, 2004) combines two common cognitive control paradigms, task switching and working memory span, to investigate the integration of plan-level and task-level processes during control of sequential behavior. The current study expands past task span research to include measures of encoding processes and choice behavior with volitional sequence generation, using the standard task span as well as a novel voluntary task span paradigm. In two experiments, we consider how sequence complexity, defined separately for plan-level and task-level complexity, influences sequence encoding (Experiment 1), sequence choice (Experiment 2), sequence memory, and task performance of planned sequences of action. Results indicate that participants were sensitive to sequence complexity, but that different aspects of behavior are most strongly influenced by different types of complexity. Hierarchical complexity at the plan level best predicts voluntary sequence generation and memory; while switch frequency at the task level best predicts encoding of externally defined sequences and task performance. Furthermore, performance RTs were similar for externally and internally defined plans, whereas memory was improved for internally defined sequences. Finally, participants demonstrated a significant sequence choice bias in the voluntary task span. Consistent with past research on choice behavior, volitional selection of plans was markedly influenced by both the ease of memory and performance.

Illuminating the inner leadership journey by engaging intention and mindfulness as guided by caring theory.

PubMed

Pipe, Teresa Britt

2008-01-01

Sustained, high-performance nursing leadership can be effectively guided by caring theory. While much of leadership performance is manifested by external behaviors, highly effective leaders are also grounded by internal work of self-reflection and growth. This article focuses primarily on the inward journey of leadership as guided by Jean Watson's Theory of Human Caring. Key elements of the theory are interpreted within the context of the emerging, urgent, high-stakes challenges of the current healthcare environment. The links between self-nurturance and caring-healing leadership of others are explored.

Ecosystems, Teacher's Guide.

ERIC Educational Resources Information Center

California Univ., Berkeley. Science Curriculum Improvement Study.

The Science Curriculum Improvement Study has developed this teacher's guide to "Ecosystems," the sixth part of a six unit life science curriculum sequence. The six basic units, emphasizing organism-environment interactions, are organisms, life cycles, populations, environments, communities, and ecosystems. They make use of scientific and…

Populations, Teacher's Guide.

ERIC Educational Resources Information Center

California Univ., Berkeley. Science Curriculum Improvement Study.

The Science Curriculum Improvement Study has developed this teacher's guide to "Populations," the third part of a six-unit life science curriculum sequence. The six basic units, emphasizing organism-environment interactions, are organisms, life cycles, populations, environments, communities, and ecosystems; and they make use of…

Communities, Teacher's Guide.

ERIC Educational Resources Information Center

California Univ., Berkeley. Science Curriculum Improvement Study.

The Science Curriculum Improvement Study has developed this teacher's guide to "Communities," the fifth part of a six unit life science curriculum sequence. The six basic units, emphasizing organism-environment interactions, are organisms, life cycles, populations, environments, communities, and ecosystems, and make use of scientific and…

Ultrasonographic percutaneous anatomy of the atlanto-occipital region and indirect ultrasound-guided cisternal puncture in the dog and the cat.

PubMed

Etienne, A-L; Audigié, F; Peeters, D; Gabriel, A; Busoni, V

2015-04-01

Cisternal puncture in dogs and cats is commonly carried out. This article describes the percutaneous ultrasound anatomy of the cisternal region in the dog and the cat and an indirect technique for ultrasound-guided cisternal puncture. Ultrasound images obtained ex vivo and in vivo were compared with anatomic sections and used to identify the landmarks for ultrasound-guided cisternal puncture. The ultrasound-guided procedure was established in cadavers and then applied in vivo in seven dogs and two cats. The anatomic landmarks for the ultrasound-guided puncture are the cisterna magna, the spinal cord, the two occipital condyles on transverse images, the external occipital crest and the dorsal arch of the first cervical vertebra on longitudinal images. Using these ultrasound anatomic landmarks, an indirect ultrasound-guided technique for cisternal puncture is applicable in the dog and the cat. © 2014 Blackwell Verlag GmbH.

The status of Fast Ignition Realization Experiment (FIREX) and prospects for inertial fusion energy

NASA Astrophysics Data System (ADS)

Azechi, H.; FIREX Project Team

2016-05-01

Here we report recent progress for the fast ignition inertial confinement fusion demonstration. The fraction of low energy (< 1 MeV) component of the relativistic electron beam (REB), which efficiently heats the fuel core, increases by a factor of 4 by enhancing pulse contrast of heating laser and removing preformed plasma sources. Kilo-tesla magnetic field is studied to guide the diverging REB to the fuel core. The transport simulation of the REB accelerated by the heating laser in the externally applied and compressed magnetic field indicates that the REB can be guided efficiently to the fuel core. The integrated simulation shows > 4% of the heating efficiency and > 4 keV of ion temperature are achievable by using GEKKO-XII and LFEX, properly designed cone-fuel and an external magnetic field.

Flow-orthogonal bead oscillation in a microfluidic chip with a magnetic anisotropic flux-guide array.

PubMed

van Pelt, Stijn; Derks, Roy; Matteucci, Marco; Hansen, Mikkel Fougt; Dietzel, Andreas

2011-04-01

A new concept for the manipulation of superparamagnetic beads inside a microfluidic chip is presented in this paper. The concept allows for bead actuation orthogonal to the flow direction inside a microchannel. Basic manipulation functionalities were studied by means of finite element simulations and results were oval-shaped steady state oscillations with bead velocities up to 500 μm/s. The width of the trajectory could be controlled by prescribing external field rotation. Successful verification experiments were performed on a prototype chip fabricated with excimer laser ablation in polycarbonate and electroforming of nickel flux-guides. Bead velocities up to 450 μm/s were measured in a 75 μm wide channel. By prescribing the currents in the external quadrupole magnet, the shape of the bead trajectory could be controlled.

External heat transfer predictions in a highly loaded transonic linear turbine guide vane cascade using an upwind biased Navier-Stokes solver

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

Gehrer, A.; Jericha, H.

External heat transfer predictions are performed for two-dimensional turbine blade cascades. The Reynolds-averaged Navier-Stokes equations with algebraic (Arnone and Pacciani, 1998), one-equation (Spalart and Allmaras, 1994), and two-equation (low-Re {kappa}-{epsilon}, Biswas and Fukuyama, 1994) turbulence closures are solved with a fully implicit time-marching finite volume method. Comparisons with measurements (Arts et al., 1990; Arts, 1994) for a highly loaded transonic turbine nozzle guide vane cascade show good agreement in some cases, but also reveal problems with transition prediction and turbulence modeling. Special attention has been focused on the low-Re {kappa}-{epsilon} model concerning the influence of the inlet boundary condition formore » the {epsilon}-equation and problems in the stagnation point region.« less

Sequence information signal processor for local and global string comparisons

DOEpatents

Peterson, John C.; Chow, Edward T.; Waterman, Michael S.; Hunkapillar, Timothy J.

1997-01-01

A sequence information signal processing integrated circuit chip designed to perform high speed calculation of a dynamic programming algorithm based upon the algorithm defined by Waterman and Smith. The signal processing chip of the present invention is designed to be a building block of a linear systolic array, the performance of which can be increased by connecting additional sequence information signal processing chips to the array. The chip provides a high speed, low cost linear array processor that can locate highly similar global sequences or segments thereof such as contiguous subsequences from two different DNA or protein sequences. The chip is implemented in a preferred embodiment using CMOS VLSI technology to provide the equivalent of about 400,000 transistors or 100,000 gates. Each chip provides 16 processing elements, and is designed to provide 16 bit, two's compliment operation for maximum score precision of between -32,768 and +32,767. It is designed to provide a comparison between sequences as long as 4,194,304 elements without external software and between sequences of unlimited numbers of elements with the aid of external software. Each sequence can be assigned different deletion and insertion weight functions. Each processor is provided with a similarity measure device which is independently variable. Thus, each processor can contribute to maximum value score calculation using a different similarity measure.

Load Carriage Capacity of the Dismounted Combatant - A Commanders’ Guide

DTIC Science & Technology

2012-10-01

predictive model has been used throughout this document to predict the physiological burden (i.e. energy cost ) of representative load carriage...scenarios. As a general guide this model indicates that a 10 kg increase in external load is metabolically equivalent (i.e. energy cost ) to an increase...larger increases in energy cost for a load carriage task. The multi-factorial nature of human load carriage capacity makes it difficult to set

MiDAS: the field guide to the microbes of activated sludge.

PubMed

McIlroy, Simon Jon; Saunders, Aaron Marc; Albertsen, Mads; Nierychlo, Marta; McIlroy, Bianca; Hansen, Aviaja Anna; Karst, Søren Michael; Nielsen, Jeppe Lund; Nielsen, Per Halkjær

2015-01-01

The Microbial Database for Activated Sludge (MiDAS) field guide is a freely available online resource linking the identity of abundant and process critical microorganisms in activated sludge wastewater treatment systems to available data related to their functional importance. Phenotypic properties of some of these genera are described, but most are known only from sequence data. The MiDAS taxonomy is a manual curation of the SILVA taxonomy that proposes a name for all genus-level taxa observed to be abundant by large-scale 16 S rRNA gene amplicon sequencing of full-scale activated sludge communities. The taxonomy can be used to classify unknown sequences, and the online MiDAS field guide links the identity to the available information about their morphology, diversity, physiology and distribution. The use of a common taxonomy across the field will provide a solid foundation for the study of microbial ecology of the activated sludge process and related treatment processes. The online MiDAS field guide is a collaborative workspace intended to facilitate a better understanding of the ecology of activated sludge and related treatment processes--knowledge that will be an invaluable resource for the optimal design and operation of these systems. © The Author(s) 2015. Published by Oxford University Press.

MiDAS: the field guide to the microbes of activated sludge

PubMed Central

McIlroy, Simon Jon; Saunders, Aaron Marc; Albertsen, Mads; Nierychlo, Marta; McIlroy, Bianca; Hansen, Aviaja Anna; Karst, Søren Michael; Nielsen, Jeppe Lund; Nielsen, Per Halkjær

2015-01-01

The Microbial Database for Activated Sludge (MiDAS) field guide is a freely available online resource linking the identity of abundant and process critical microorganisms in activated sludge wastewater treatment systems to available data related to their functional importance. Phenotypic properties of some of these genera are described, but most are known only from sequence data. The MiDAS taxonomy is a manual curation of the SILVA taxonomy that proposes a name for all genus-level taxa observed to be abundant by large-scale 16 S rRNA gene amplicon sequencing of full-scale activated sludge communities. The taxonomy can be used to classify unknown sequences, and the online MiDAS field guide links the identity to the available information about their morphology, diversity, physiology and distribution. The use of a common taxonomy across the field will provide a solid foundation for the study of microbial ecology of the activated sludge process and related treatment processes. The online MiDAS field guide is a collaborative workspace intended to facilitate a better understanding of the ecology of activated sludge and related treatment processes—knowledge that will be an invaluable resource for the optimal design and operation of these systems. Database URL: http://www.midasfieldguide.org PMID:26120139

What Do Biochemistry Students Pay Attention to in External Representations of Protein Translation? Tthe Case of the Shine-Dalgarno Sequence

ERIC Educational Resources Information Center

Bussey, Thomas J.; Orgill, MaryKay

2015-01-01

Biochemistry instructors often use external representations--ranging from static diagrams to dynamic animations and from simplistic, stylized illustrations to more complex, realistic presentations--to help their students visualize abstract cellular and molecular processes, mechanisms, and components. However, relatively little is known about how…

Internal and External Focus of Attention in a Novice Form Sport

ERIC Educational Resources Information Center

Lawrence, Gavin P.; Gottwald, Vicky M.; Hardy, James; Khan, Michael A.

2011-01-01

In the current experiment, we examined optimal focus for novices during a movement sequence in which performance was measured on accurate movement form/technique. A novel gymnastics routine was practiced under either an internal skill-relevant, internal skill-irrelevant, external, or no attention focus. Retention and transfer tests were then…

Echoes of China.

ERIC Educational Resources Information Center

Chang, Pei-lan Li; Chao, Johanna T.; Chao, Yenshew Lynn; Chin, Ai-li S.; Hsieh, Charlotte Sheau-mann; Sun, Paul P.; Swartz, Leslie M.; Wang, Theresa; Wu, Fa Y.

This curriculum guide is developed to accompany 7 Chinese Cultural Heritage kits for use in intermediate and middle school classrooms. The units in this guide may be used with or without the accompanying kits. When appropriate, units include: objectives, introductory information, suggested presentation sequence, activity instruction, evaluation…

Aviation Maintenance Technology. General. Curriculum Implementation Guide.

ERIC Educational Resources Information Center

Moore, John, Jr.; And Others

This curriculum implementation guide is a scope and sequence for the general section of a course in aviation maintenance technology. The course materials were prepared through a cooperative effort of airframe and powerplant mechanics, general aviation industry representatives, Federal Aviation Administration representatives, and vocational…

Sequence-encoded colloidal origami and microbot assemblies from patchy magnetic cubes

PubMed Central

Han, Koohee; Shields, C. Wyatt; Diwakar, Nidhi M.; Bharti, Bhuvnesh; López, Gabriel P.; Velev, Orlin D.

2017-01-01

Colloidal-scale assemblies that reconfigure on demand may serve as the next generation of soft “microbots,” artificial muscles, and other biomimetic devices. This requires the precise arrangement of particles into structures that are preprogrammed to reversibly change shape when actuated by external fields. The design and making of colloidal-scale assemblies with encoded directional particle-particle interactions remain a major challenge. We show how assemblies of metallodielectric patchy microcubes can be engineered to store energy through magnetic polarization and release it on demand by microscale reconfiguration. The dynamic pattern of folding and reconfiguration of the chain-like assemblies can be encoded in the sequence of the cube orientation. The residual polarization of the metallic facets on the microcubes leads to local interactions between the neighboring particles, which is directed by the conformational restrictions of their shape after harvesting energy from external magnetic fields. These structures can also be directionally moved, steered, and maneuvered by global forces from external magnetic fields. We illustrate these capabilities by examples of assemblies of specific sequences that can be actuated, reoriented, and spatially maneuvered to perform microscale operations such as capturing and transporting live cells, acting as prototypes of microbots, micromixers, and other active microstructures. PMID:28798960

Methodologic European external quality assurance for DNA sequencing: the EQUALseq program.

PubMed

Ahmad-Nejad, Parviz; Dorn-Beineke, Alexandra; Pfeiffer, Ulrike; Brade, Joachim; Geilenkeuser, Wolf-Jochen; Ramsden, Simon; Pazzagli, Mario; Neumaier, Michael

2006-04-01

DNA sequencing is a key technique in molecular diagnostics, but to date no comprehensive methodologic external quality assessment (EQA) programs have been instituted. Between 2003 and 2005, the European Union funded, as specific support actions, the EQUAL initiative to develop methodologic EQA schemes for genotyping (EQUALqual), quantitative PCR (EQUALquant), and sequencing (EQUALseq). Here we report on the results of the EQUALseq program. The participating laboratories received a 4-sample set comprising 2 DNA plasmids, a PCR product, and a finished sequencing reaction to be analyzed. Data and information from detailed questionnaires were uploaded online and evaluated by use of a scoring system for technical skills and proficiency of data interpretation. Sixty laboratories from 21 European countries registered, and 43 participants (72%) returned data and samples. Capillary electrophoresis was the predominant platform (n = 39; 91%). The median contiguous correct sequence stretch was 527 nucleotides with considerable variation in quality of both primary data and data evaluation. The association between laboratory performance and the number of sequencing assays/year was statistically significant (P <0.05). Interestingly, more than 30% of participants neither added comments to their data nor made efforts to identify the gene sequences or mutational positions. Considerable variations exist even in a highly standardized methodology such as DNA sequencing. Methodologic EQAs are appropriate tools to uncover strengths and weaknesses in both technique and proficiency, and our results emphasize the need for mandatory EQAs. The results of EQUALseq should help improve the overall quality of molecular genetics findings obtained by DNA sequencing.

[External evaluation of population-based cancer registries: the REDEPICAN Guide for Latin America].

PubMed

Navarro, Carmen; Molina, José Antonio; Barrios, Enrique; Izarzugaza, Isabel; Loria, Dora; Cueva, Patricia; Sánchez, María José; Chirlaque, María Dolores; Fernández, Leticia

2013-11-01

Evaluate the feasibility of the REDEPICAN Guide (Red Iberoamericana de Epidemiología y Sistemas de Información en Cáncer) and its adaptation to the current situation of population-based cancer registries (PBCRs) in Latin America and the Caribbean as a useful tool to improve these registries. Experts in cancer registries and health audits designed the guide and developed seven domains to evaluate in PBCRs. Several criteria were selected for each domain, with corresponding standards, scored according to three levels of compliance. Two training courses for external evaluators and three discussion panels for experts were organized. The guide was tested in six PBCRs in Latin America and Spain. The guide contains 68 criteria, 10 of which are considered essential for a PBCR. Based on its score, a registry is regarded as acceptable (41-199), good (200-299), or excellent (300-350). The registry methods domain accounts for 25% of the score, followed by completeness and validity (19%), dissemination of outcomes (19%), structure (13%), confidentiality and ethical aspects (11%), comparability (9%), and the procedures manual (3%). The pilot project enabled (1) enhancement of criteria and standards, (2) expansion of the quality concept to include client needs, and (3) strengthening the dissemination of outcomes section. Two of the Latin American registries that were evaluated improved their quality, meeting the standards of the International Agency for Research on Cancer. Development of the REDEPICAN Guide has taken into account the context of the registries in Latin America and is a useful and innovative tool for improving the quality of PBCRs. Furthermore, it is ready for use in other countries and registries.

Optofluidic encapsulation and manipulation of silicon microchips using image processing based optofluidic maskless lithography and railed microfluidics.

PubMed

Chung, Su Eun; Lee, Seung Ah; Kim, Jiyun; Kwon, Sunghoon

2009-10-07

We demonstrate optofluidic encapsulation of silicon microchips using image processing based optofluidic maskless lithography and manipulation using railed microfluidics. Optofluidic maskless lithography is a dynamic photopolymerization technique of free-floating microstructures within a fluidic channel using spatial light modulator. Using optofluidic maskless lithography via computer-vision aided image processing, polymer encapsulants are fabricated for chip protection and guiding-fins for efficient chip conveying within a fluidic channel. Encapsulated silicon chips with guiding-fins are assembled using railed microfluidics, which is an efficient guiding and heterogeneous self-assembly system of microcomponents. With our technology, externally fabricated silicon microchips are encapsulated, fluidically guided and self-assembled potentially enabling low cost fluidic manipulation and assembly of integrated circuits.

Space-Based Observations of Satellites From the MOST Microsatellite

DTIC Science & Technology

2006-11-01

error estimate for these observations. To perform differential photometry, reference magnitudes for the background stars are needed. The Hubble Guide ...22 6.3 External Calibration References ..................................................................... 23 6.4 Post...32 10. References

Cooperative Crisis Management and Avian Influenza. A Risk Assessment Guide for International Contagious Disease Prevention and Risk Mitigation

DTIC Science & Technology

2006-03-01

with a decrease in trade restrictions between neighboring countries, make it easier for microbes , disease- causing insects, and infected animals to...with a collection of information if it does not display a currently valid OMB control number. 1. REPORT DATE MAR 2006 2. REPORT TYPE 3. DATES COVERED...are important aspects of managing external perceptions. External perceptions can cause unaffected countries to consider more drastic measures for

A programmable Cas9-serine recombinase fusion protein that operates on DNA sequences in mammalian cells

PubMed Central

Chaikind, Brian; Bessen, Jeffrey L.; Thompson, David B.; Hu, Johnny H.; Liu, David R.

2016-01-01

We describe the development of ‘recCas9’, an RNA-programmed small serine recombinase that functions in mammalian cells. We fused a catalytically inactive dCas9 to the catalytic domain of Gin recombinase using an optimized fusion architecture. The resulting recCas9 system recombines DNA sites containing a minimal recombinase core site flanked by guide RNA-specified sequences. We show that these recombinases can operate on DNA sites in mammalian cells identical to genomic loci naturally found in the human genome in a manner that is dependent on the guide RNA sequences. DNA sequencing reveals that recCas9 catalyzes guide RNA-dependent recombination in human cells with an efficiency as high as 32% on plasmid substrates. Finally, we demonstrate that recCas9 expressed in human cells can catalyze in situ deletion between two genomic sites. Because recCas9 directly catalyzes recombination, it generates virtually no detectable indels or other stochastic DNA modification products. This work represents a step toward programmable, scarless genome editing in unmodified cells that is independent of endogenous cellular machinery or cell state. Current and future generations of recCas9 may facilitate targeted agricultural breeding, or the study and treatment of human genetic diseases. PMID:27515511

Toward a General Approach for RNA-Templated Hierarchical Assembly of Split-Proteins

PubMed Central

Furman, Jennifer L.; Badran, Ahmed H.; Ajulo, Oluyomi; Porter, Jason R.; Stains, Cliff I.; Segal, David J.; Ghosh, Indraneel

2010-01-01

The ability to conditionally turn on a signal or induce a function in the presence of a user-defined RNA target has potential applications in medicine and synthetic biology. Although sequence-specific pumilio repeat proteins can target a limited set of ssRNA sequences, there are no general methods for targeting ssRNA with designed proteins. As a first step toward RNA recognition, we utilized the RNA binding domain of argonaute, implicated in RNA interference, for specifically targeting generic 2-nucleotide, 3' overhangs of any dsRNA. We tested the reassembly of a split-luciferase enzyme guided by argonaute-mediated recognition of newly generated nucleotide overhangs when ssRNA is targeted by a designed complementary guide sequence. This approach was successful when argonaute was utilized in conjunction with a pumilio repeat and expanded the scope of potential ssRNA targets. However, targeting any desired ssRNA remained elusive as two argonaute domains provided minimal reassembled split-luciferase. We next designed and tested a second hierarchical assembly, wherein ssDNA guides are appended to DNA hairpins that serve as a scaffold for high affinity zinc fingers attached to split-luciferase. In the presence of a ssRNA target containing adjacent sequences complementary to the guides, the hairpins are brought into proximity, allowing for zinc finger binding and concomitant reassembly of the fragmented luciferase. The scope of this new approach was validated by specifically targeting RNA encoding VEGF, hDM2, and HER2. These approaches provide potentially general design paradigms for the conditional reassembly of fragmented proteins in the presence of any desired ssRNA target. PMID:20681585

Preoperative magnetic resonance imaging protocol for endoscopic cranial base image-guided surgery.

PubMed

Grindle, Christopher R; Curry, Joseph M; Kang, Melissa D; Evans, James J; Rosen, Marc R

2011-01-01

Despite the increasing utilization of image-guided surgery, no radiology protocols for obtaining magnetic resonance (MR) imaging of adequate quality are available in the current literature. At our institution, more than 300 endonasal cranial base procedures including pituitary, extended pituitary, and other anterior skullbase procedures have been performed in the past 3 years. To facilitate and optimize preoperative evaluation and assessment, there was a need to develop a magnetic resonance protocol. Retrospective Technical Assessment was performed. Through a collaborative effort between the otolaryngology, neurosurgery, and neuroradiology departments at our institution, a skull base MR image-guided (IGS) protocol was developed with several ends in mind. First, it was necessary to generate diagnostic images useful for the more frequently seen pathologies to improve work flow and limit the expense and inefficiency of case specific MR studies. Second, it was necessary to generate sequences useful for IGS, preferably using sequences that best highlight that lesion. Currently, at our institution, all MR images used for IGS are obtained using this protocol as part of preoperative planning. The protocol that has been developed allows for thin cut precontrast and postcontrast axial cuts that can be used to plan intraoperative image guidance. It also obtains a thin cut T2 axial series that can be compiled separately for intraoperative imaging, or may be fused with computed tomographic images for combined modality. The outlined protocol obtains image sequences effective for diagnostic and operative purposes for image-guided surgery using both T1 and T2 sequences. Copyright © 2011 Elsevier Inc. All rights reserved.

Science Guide for Secondary Schools.

ERIC Educational Resources Information Center

Georgia State Dept. of Education, Atlanta. Office of Instructional Services.

This six-chapter guide is designed to help Georgia teachers adopt or adapt various options into the local school's science curriculum. Major areas addressed in the chapters are: (1) secondary school curriculum development (focusing on performance objectives, sequencing the curriculum, evaluation, and scientific literacy); (2) teaching methods…

Structure of yeast Argonaute with guide RNA

PubMed Central

Nakanishi, Kotaro; Weinberg, David E.; Bartel, David P.; Patel, Dinshaw J.

2012-01-01

The RNA-induced silencing complex, comprising Argonaute and guide RNA, mediates RNA interference. Here we report the 3.2 Å crystal structure of Kluyveromyces Argonaute (KpAGO) fortuitously complexed with guide RNA originating from small-RNA duplexes autonomously loaded and processed by recombinant KpAGO. Despite their diverse sequences, guide-RNA nucleotides 1–8 are positioned similarly, with sequence-independent contacts to bases, phosphates and 2′-hydroxyl groups pre-organizing the backbone of nucleotides 2–8 in a near–A-form conformation. Compared with prokaryotic Argonautes, KpAGO has numerous surface-exposed insertion segments, with a cluster of conserved insertions repositioning the N domain to enable full propagation of guide–target pairing. Compared with Argonautes in inactive conformations, KpAGO has a hydrogen-bond network that stabilizes an expanded and repositioned loop, which inserts an invariant glutamate into the catalytic pocket. Mutation analyses and analogies to Ribonuclease H indicate that insertion of this glutamate finger completes a universally conserved catalytic tetrad, thereby activating Argonaute for RNA cleavage. PMID:22722195

Phylogeny-guided (meta)genome mining approach for the targeted discovery of new microbial natural products.

PubMed

Kang, Hahk-Soo

2017-02-01

Genomics-based methods are now commonplace in natural products research. A phylogeny-guided mining approach provides a means to quickly screen a large number of microbial genomes or metagenomes in search of new biosynthetic gene clusters of interest. In this approach, biosynthetic genes serve as molecular markers, and phylogenetic trees built with known and unknown marker gene sequences are used to quickly prioritize biosynthetic gene clusters for their metabolites characterization. An increase in the use of this approach has been observed for the last couple of years along with the emergence of low cost sequencing technologies. The aim of this review is to discuss the basic concept of a phylogeny-guided mining approach, and also to provide examples in which this approach was successfully applied to discover new natural products from microbial genomes and metagenomes. I believe that the phylogeny-guided mining approach will continue to play an important role in genomics-based natural products research.

Improving CRISPR–Cas specificity with chemical modifications in single-guide RNAs

PubMed Central

Ryan, Daniel E; Taussig, David; Steinfeld, Israel; Phadnis, Smruti M; Lunstad, Benjamin D; Singh, Madhurima; Vuong, Xuan; Okochi, Kenji D; McCaffrey, Ryan; Olesiak, Magdalena; Roy, Subhadeep; Yung, Chong Wing; Curry, Bo; Sampson, Jeffrey R; Dellinger, Douglas J

2018-01-01

Abstract CRISPR systems have emerged as transformative tools for altering genomes in living cells with unprecedented ease, inspiring keen interest in increasing their specificity for perfectly matched targets. We have developed a novel approach for improving specificity by incorporating chemical modifications in guide RNAs (gRNAs) at specific sites in their DNA recognition sequence (‘guide sequence’) and systematically evaluating their on-target and off-target activities in biochemical DNA cleavage assays and cell-based assays. Our results show that a chemical modification (2′-O-methyl-3′-phosphonoacetate, or ‘MP’) incorporated at select sites in the ribose-phosphate backbone of gRNAs can dramatically reduce off-target cleavage activities while maintaining high on-target performance, as demonstrated in clinically relevant genes. These findings reveal a unique method for enhancing specificity by chemically modifying the guide sequence in gRNAs. Our approach introduces a versatile tool for augmenting the performance of CRISPR systems for research, industrial and therapeutic applications. PMID:29216382

Fluoroscopic tumor tracking for image-guided lung cancer radiotherapy

NASA Astrophysics Data System (ADS)

Lin, Tong; Cerviño, Laura I.; Tang, Xiaoli; Vasconcelos, Nuno; Jiang, Steve B.

2009-02-01

Accurate lung tumor tracking in real time is a keystone to image-guided radiotherapy of lung cancers. Existing lung tumor tracking approaches can be roughly grouped into three categories: (1) deriving tumor position from external surrogates; (2) tracking implanted fiducial markers fluoroscopically or electromagnetically; (3) fluoroscopically tracking lung tumor without implanted fiducial markers. The first approach suffers from insufficient accuracy, while the second may not be widely accepted due to the risk of pneumothorax. Previous studies in fluoroscopic markerless tracking are mainly based on template matching methods, which may fail when the tumor boundary is unclear in fluoroscopic images. In this paper we propose a novel markerless tumor tracking algorithm, which employs the correlation between the tumor position and surrogate anatomic features in the image. The positions of the surrogate features are not directly tracked; instead, we use principal component analysis of regions of interest containing them to obtain parametric representations of their motion patterns. Then, the tumor position can be predicted from the parametric representations of surrogates through regression. Four regression methods were tested in this study: linear and two-degree polynomial regression, artificial neural network (ANN) and support vector machine (SVM). The experimental results based on fluoroscopic sequences of ten lung cancer patients demonstrate a mean tracking error of 2.1 pixels and a maximum error at a 95% confidence level of 4.6 pixels (pixel size is about 0.5 mm) for the proposed tracking algorithm.

Dynamic T2-mapping during magnetic resonance guided high intensity focused ultrasound ablation of bone marrow

NASA Astrophysics Data System (ADS)

Waspe, Adam C.; Looi, Thomas; Mougenot, Charles; Amaral, Joao; Temple, Michael; Sivaloganathan, Siv; Drake, James M.

2012-11-01

Focal bone tumor treatments include amputation, limb-sparing surgical excision with bone reconstruction, and high-dose external-beam radiation therapy. Magnetic resonance guided high intensity focused ultrasound (MR-HIFU) is an effective non-invasive thermotherapy for palliative management of bone metastases pain. MR thermometry (MRT) measures the proton resonance frequency shift (PRFS) of water molecules and produces accurate (<1°C) and dynamic (<5s) thermal maps in soft tissues. PRFS-MRT is ineffective in fatty tissues such as yellow bone marrow and, since accurate temperature measurements are required in the bone to ensure adequate thermal dose, MR-HIFU is not indicated for primary bone tumor treatments. Magnetic relaxation times are sensitive to lipid temperature and we hypothesize that bone marrow temperature can be determined accurately by measuring changes in T2, since T2 increases linearly in fat during heating. T2-mapping using dual echo times during a dynamic turbo spin-echo pulse sequence enabled rapid measurement of T2. Calibration of T2-based thermal maps involved heating the marrow in a bovine femur and simultaneously measuring T2 and temperature with a thermocouple. A positive T2 temperature dependence in bone marrow of 20 ms/°C was observed. Dynamic T2-mapping should enable accurate temperature monitoring during MR-HIFU treatment of bone marrow and shows promise for improving the safety and reducing the invasiveness of pediatric bone tumor treatments.

Adaptive pattern for autonomous UAV guidance

NASA Astrophysics Data System (ADS)

Sung, Chen-Ko; Segor, Florian

2013-09-01

The research done at the Fraunhofer IOSB in Karlsruhe within the AMFIS project is focusing on a mobile system to support rescue forces in accidents or disasters. The system consists of a ground control station which has the capability to communicate with a large number of heterogeneous sensors and sensor carriers and provides several open interfaces to allow easy integration of additional sensors into the system. Within this research we focus mainly on UAV such as VTOL (Vertical takeoff and Landing) systems because of their ease of use and their high maneuverability. To increase the positioning capability of the UAV, different onboard processing chains of image exploitation for real time detection of patterns on the ground and the interfacing technology for controlling the UAV from the payload during flight were examined. The earlier proposed static ground pattern was extended by an adaptive component which admits an additional visual communication channel to the aircraft. For this purpose different components were conceived to transfer additive information using changeable patterns on the ground. The adaptive ground pattern and their application suitability had to be tested under external influence. Beside the adaptive ground pattern, the onboard process chains and the adaptations to the demands of changing patterns are introduced in this paper. The tracking of the guiding points, the UAV navigation and the conversion of the guiding point positions from the images to real world co-ordinates in video sequences, as well as use limits and the possibilities of an adaptable pattern are examined.

SEQassembly: A Practical Tools Program for Coding Sequences Splicing

NASA Astrophysics Data System (ADS)

Lee, Hongbin; Yang, Hang; Fu, Lei; Qin, Long; Li, Huili; He, Feng; Wang, Bo; Wu, Xiaoming

CDS (Coding Sequences) is a portion of mRNA sequences, which are composed by a number of exon sequence segments. The construction of CDS sequence is important for profound genetic analysis such as genotyping. A program in MATLAB environment is presented, which can process batch of samples sequences into code segments under the guide of reference exon models, and splice these code segments of same sample source into CDS according to the exon order in queue file. This program is useful in transcriptional polymorphism detection and gene function study.

CRISPR/Cas9 in Genome Editing and Beyond.

PubMed

Wang, Haifeng; La Russa, Marie; Qi, Lei S

2016-06-02

The Cas9 protein (CRISPR-associated protein 9), derived from type II CRISPR (clustered regularly interspaced short palindromic repeats) bacterial immune systems, is emerging as a powerful tool for engineering the genome in diverse organisms. As an RNA-guided DNA endonuclease, Cas9 can be easily programmed to target new sites by altering its guide RNA sequence, and its development as a tool has made sequence-specific gene editing several magnitudes easier. The nuclease-deactivated form of Cas9 further provides a versatile RNA-guided DNA-targeting platform for regulating and imaging the genome, as well as for rewriting the epigenetic status, all in a sequence-specific manner. With all of these advances, we have just begun to explore the possible applications of Cas9 in biomedical research and therapeutics. In this review, we describe the current models of Cas9 function and the structural and biochemical studies that support it. We focus on the applications of Cas9 for genome editing, regulation, and imaging, discuss other possible applications and some technical considerations, and highlight the many advantages that CRISPR/Cas9 technology offers.

Identification of Stochastically Perturbed Autonomous Systems from Temporal Sequences of Probability Density Functions

NASA Astrophysics Data System (ADS)

Nie, Xiaokai; Luo, Jingjing; Coca, Daniel; Birkin, Mark; Chen, Jing

2018-03-01

The paper introduces a method for reconstructing one-dimensional iterated maps that are driven by an external control input and subjected to an additive stochastic perturbation, from sequences of probability density functions that are generated by the stochastic dynamical systems and observed experimentally.

EGASP: the human ENCODE Genome Annotation Assessment Project

PubMed Central

Guigó, Roderic; Flicek, Paul; Abril, Josep F; Reymond, Alexandre; Lagarde, Julien; Denoeud, France; Antonarakis, Stylianos; Ashburner, Michael; Bajic, Vladimir B; Birney, Ewan; Castelo, Robert; Eyras, Eduardo; Ucla, Catherine; Gingeras, Thomas R; Harrow, Jennifer; Hubbard, Tim; Lewis, Suzanna E; Reese, Martin G

2006-01-01

Background We present the results of EGASP, a community experiment to assess the state-of-the-art in genome annotation within the ENCODE regions, which span 1% of the human genome sequence. The experiment had two major goals: the assessment of the accuracy of computational methods to predict protein coding genes; and the overall assessment of the completeness of the current human genome annotations as represented in the ENCODE regions. For the computational prediction assessment, eighteen groups contributed gene predictions. We evaluated these submissions against each other based on a 'reference set' of annotations generated as part of the GENCODE project. These annotations were not available to the prediction groups prior to the submission deadline, so that their predictions were blind and an external advisory committee could perform a fair assessment. Results The best methods had at least one gene transcript correctly predicted for close to 70% of the annotated genes. Nevertheless, the multiple transcript accuracy, taking into account alternative splicing, reached only approximately 40% to 50% accuracy. At the coding nucleotide level, the best programs reached an accuracy of 90% in both sensitivity and specificity. Programs relying on mRNA and protein sequences were the most accurate in reproducing the manually curated annotations. Experimental validation shows that only a very small percentage (3.2%) of the selected 221 computationally predicted exons outside of the existing annotation could be verified. Conclusion This is the first such experiment in human DNA, and we have followed the standards established in a similar experiment, GASP1, in Drosophila melanogaster. We believe the results presented here contribute to the value of ongoing large-scale annotation projects and should guide further experimental methods when being scaled up to the entire human genome sequence. PMID:16925836

Guiding-center equations for electrons in ultraintense laser fields

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

Moore, J.E.; Fisch, N.J.

1994-01-01

The guiding-center equations are derived for electrons in arbitrarily intense laser fields also subject to external fields and ponderomotive forces. Exhibiting the relativistic mass increase of the oscillating electrons, a simple frame-invariant equation is shown to govern the behavior of the electrons for sufficiently weak background fields and ponderomotive forces. The parameter regime for which such a formulation is valid is made precise, and some predictions of the equation are checked by numerical simulation.

A user's guide to the Flexible Spacecraft Dynamics and Control Program

NASA Technical Reports Server (NTRS)

Fedor, J. V.

1984-01-01

A guide to the use of the Flexible Spacecraft Dynamics Program (FSD) is presented covering input requirements, control words, orbit generation, spacecraft description and simulation options, and output definition. The program can be used in dynamics and control analysis as well as in orbit support of deployment and control of spacecraft. The program is applicable to inertially oriented spinning, Earth oriented or gravity gradient stabilized spacecraft. Internal and external environmental effects can be simulated.

Electrode carrying wire for GTAW welding

NASA Technical Reports Server (NTRS)

Morgan, Gene E. (Inventor); Dyer, Gerald E. (Inventor)

1990-01-01

A welding torch for gas tungsten arc welding apparatus has a hollow tungsten electrode including a ceramic liner and forms the filler metal wire guide. The wire is fed through the tungsten electrode thereby reducing the size of the torch to eliminate clearance problems which exist with external wire guides. Since the wire is preheated from the tungsten more wire may be fed into the weld puddle, and the wire will not oxidize because it is always within the shielding gas.

What Is Technology Transfer? | Poster

Cancer.gov

The NCI Technology Transfer Center (TTC) facilitates partnerships between NIH research laboratories and external partners. With a team of technology transfer specialists, NCI TTC guides interactions from discovery to patenting, as well as from collaboration and invention development to licensing.

Comparison of infection between internal-external and external percutaneous transhepatic biliary drainage in treating patients with malignant obstructive jaundice.

PubMed

Xu, Chuan; Huang, Xin-En; Wang, Shu-Xiang; Lv, Peng-Hua; Sun, Ling; Wang, Fu-An

2015-01-01

Percutaneous transhepatic biliary drainage (PTBD) is a form of palliative care for patients with malignant obstructive jaundice. We here compared the infection incidence between internal-external and external drainage for patients with malignant obstructive jaundice. Patients with malignant obstructive jaundice without infection before surgery receiving internal-external or external drainage from January 2008 to July 2014 were recruited. According to percutaneous transhepatic cholangiography (PTC), if the guide wire could pass through the occlusion and enter the duodenum, we recommended internal-external drainage, and external drainage biliary drainage was set up if the occlusion was not crossed. All patients with infection after procedure received a cultivation of blood and a bile bacteriological test. Among 110 patients with malignant obstructive jaundice, 22 (52.4%) were diagnosed with infection after the procedure in the internal-external drainage group, whereas 19 (27.9%) patients were so affected in the external drainage group, the difference being significant (p<0.05). In 8 patients (36.3%) in the internal-external group infection was controlled, as compared to 12 (63.1%) in the external group (p<0.05). The mortality rate for patients with infection not controlled in internal-external group in one month was 42.8%, while this rate in external group was 28.6% (p<0.05). External drainage is a good choice, which could significantly reduce the chance of biliary infection caused by bacteria, and decrease the mortality rate at one month and improve the long-term prognosis.

Waves and Particles--The Orbital Atom, Parts One & Two of an Integrated Science Sequence, Student Guide, 1971 Edition.

ERIC Educational Resources Information Center

Portland Project Committee, OR.

The third year of the Portland Project, a three-year secondary school curriculum in integrated science, consists of four parts, the first two of which are covered in this student guide. The reading assignments for part one, "Waves and Particles," are listed in the student guide and are to be read in the Harvard Project Physics textbook.…

[Night of the Alzheimer's patient: the nightmare of the caregiver via the caregivers'guides].

PubMed

Ostrowski, Madeleine; Mietkiewicz, Marie-Claude

2015-06-01

Care for Alzheimers' patients is quite a burden on the caregivers. Guides have been devoted to improve their knowledge about the disease and to help to provide the best care for the patient. A recent study on the reluctance of caregivers'spouses to seek external help, shows that none of 31 spouses had read a caregiver's guide. The aim of this study was to assess if caregiver's guides would help caregivers to deal with sleep/wake disorders. Amongst the 46 French guides, published between 1988 and 2013, thirty three raised the subject of the night sleep with more or less details. In these guides sleep disturbances are considered either as a symptom to be monitored or a natural aging process to be supported. We made a survey of the content of the caregiver's guides, of their goals and why they have been designed to. Then we analyze how the night sleep issue is dealt with in the guides, and eventually we consider the place to be granted to the patient in the management of his/her sleep disturbances.

Accelerated Radiation-Damping for Increased Spin Equilibrium (ARISE)

PubMed Central

Huang, Susie Y.; Witzel, Thomas; Wald, Lawrence L.

2008-01-01

Control of the longitudinal magnetization in fast gradient echo sequences is an important factor enabling the high efficiency of balanced Steady State Free Precession (bSSFP) sequences. We introduce a new method for accelerating the return of the longitudinal magnetization to the +z-axis that is independent of externally applied RF pulses and shows improved off-resonance performance. The Accelerated Radiation damping for Increased Spin Equilibrium (ARISE) method uses an external feedback circuit to strengthen the Radiation Damping (RD) field. The enhanced RD field rotates the magnetization back to the +z-axis at a rate faster than T1 relaxation. The method is characterized in gradient echo phantom imaging at 3T as a function of feedback gain, phase, and duration and compared with results from numerical simulations of the Bloch equations incorporating RD. A short period of feedback (10ms) during a refocused interval of a crushed gradient echo sequence allowed greater than 99% recovery of the longitudinal magnetization when very little T2 relaxation has time to occur. Appropriate applications might include improving navigated sequences. Unlike conventional flip-back schemes, the ARISE “flip-back” is generated by the spins themselves, thereby offering a potentially useful building block for enhancing gradient echo sequences. PMID:18956463

Discovering frequently recurring movement sequences in team-sport athlete spatiotemporal data.

PubMed

Sweeting, Alice J; Aughey, Robert J; Cormack, Stuart J; Morgan, Stuart

2017-12-01

Athlete external load is typically analysed from predetermined movement thresholds. The combination of movement sequences and differences in these movements between playing positions is also currently unknown. This study developed a method to discover the frequently recurring movement sequences across playing position during matches. The external load of 12 international female netball athletes was collected by a local positioning system during four national-level matches. Velocity, acceleration and angular velocity were calculated from positional (X, Y) data, clustered via one-dimensional k-means and assigned a unique alphabetic label. Combinations of velocity, acceleration and angular velocity movement were compared using the Levenshtein distance and similarities computed by the longest common substring problem. The contribution of each movement sequence, according to playing position and relative to the wider data set, was then calculated via the Minkowski distance. A total of 10 frequently recurring combinations of movement were discovered, regardless of playing position. Only the wing attack, goal attack and goal defence playing positions are closely related. We developed a technique to discover the movement sequences, according to playing position, performed by elite netballers. This methodology can be extended to discover the frequently recurring movements within other team sports and across levels of competition.

EMR Behavioral Curriculum and Student Record.

ERIC Educational Resources Information Center

Hartnett, John J.

Intended for use as a curriculum guide, a source for objectives for the individualized educational plan, and an evaluation instrument to measure handicapped students' learning, the guide lists sequences of developmental tasks. Tasks are outlined for primary, intermediate, and secondary levels in the following areas (sample subskills in…

Business Computer Programming I. Curriculum Guide. Second Edition.

ERIC Educational Resources Information Center

Patton, Jan

This guide provides instructors of business computer programming with a curriculum correlated directly to the office education essential elements mandated by the Texas Education Agency. Introductory materials include a scope and sequence and lists of suggested textbooks, resource books, software, audiovisuals, and magazines. Eleven units are…

Bacterial Genome Engineering and Synthetic Biology: Combating Pathogens

DTIC Science & Technology

2016-11-04

engineering and SB methods such as recombineering, clustered regularly interspaced short palindromic repeats ( CRISPR ), and bacterial cell-cell...Cholera# Yersinia pseudotuberculosis# Staphylococcus aureus* Phage Engineering CRISPR /Cas9 Delivery of CRISPR genes and RNA guides for sequence...bear very close sequence alignment to the harmless strains via the use of the CRISPR /Cas9 system. The CRISPR system specifically targets a DNA sequence

Sequence Stratigraphy of the Dakota Sandstone, Eastern San Juan Basin, New Mexico, and its Relationship to Reservoir Compartmentalization

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

Varney, Peter J.

2002-04-23

This research established the Dakota-outcrop sequence stratigraphy in part of the eastern San Juan Basin, New Mexico, and relates reservoir quality lithologies in depositional sequences to structure and reservoir compartmentalization in the South Lindrith Field area. The result was a predictive tool that will help guide further exploration and development.

Experimental Influences in the Accurate Measurement of Cartilage Thickness in MRI.

PubMed

Wang, Nian; Badar, Farid; Xia, Yang

2018-01-01

Objective To study the experimental influences to the measurement of cartilage thickness by magnetic resonance imaging (MRI). Design The complete thicknesses of healthy and trypsin-degraded cartilage were measured at high-resolution MRI under different conditions, using two intensity-based imaging sequences (ultra-short echo [UTE] and multislice-multiecho [MSME]) and 3 quantitative relaxation imaging sequences (T 1 , T 2 , and T 1 ρ). Other variables included different orientations in the magnet, 2 soaking solutions (saline and phosphate buffered saline [PBS]), and external loading. Results With cartilage soaked in saline, UTE and T 1 methods yielded complete and consistent measurement of cartilage thickness, while the thickness measurement by T 2 , T 1 ρ, and MSME methods were orientation dependent. The effect of external loading on cartilage thickness is also sequence and orientation dependent. All variations in cartilage thickness in MRI could be eliminated with the use of a 100 mM PBS or imaged by UTE sequence. Conclusions The appearance of articular cartilage and the measurement accuracy of cartilage thickness in MRI can be influenced by a number of experimental factors in ex vivo MRI, from the use of various pulse sequences and soaking solutions to the health of the tissue. T 2 -based imaging sequence, both proton-intensity sequence and quantitative relaxation sequence, similarly produced the largest variations. With adequate resolution, the accurate measurement of whole cartilage tissue in clinical MRI could be utilized to detect differences between healthy and osteoarthritic cartilage after compression.

The management of vocal fold nodules in children: a national survey of speech-language pathologists.

PubMed

Signorelli, Monique E; Madill, Catherine J; McCabe, Patricia

2011-06-01

The purpose of this study was to determine the management options and voice therapy techniques currently being used by practicing speech-language pathologists (SLPs) to treat vocal fold nodules (VFNs) in children. The sources used by SLPs to inform and guide their clinical decisions when managing VFNs in children were also explored. Sixty-two SLPs completed a 23-item web-based survey. Data was analysed using frequency counts, content analyses, and supplementary analyses. SLPs reported using a range of management options and voice therapy techniques to treat VFNs in children. Voice therapy was reportedly the most frequently used management option across all respondents, with the majority of SLPs using a combination of indirect and direct voice therapy techniques. When selecting voice therapy techniques, the majority of SLPs reported that they did not use the limited external evidence available to guide their clinical decisions. Additionally, the majority of SLPs reported that they frequently relied on lower levels of evidence or non-evidence-based sources to guide clinical practice both in the presence and absence of higher quality evidence. Further research needs to investigate strategies to remove the barriers that impede SLPs use of external evidence when managing VFNs in children.

FASMA: a service to format and analyze sequences in multiple alignments.

PubMed

Costantini, Susan; Colonna, Giovanni; Facchiano, Angelo M

2007-12-01

Multiple sequence alignments are successfully applied in many studies for under- standing the structural and functional relations among single nucleic acids and protein sequences as well as whole families. Because of the rapid growth of sequence databases, multiple sequence alignments can often be very large and difficult to visualize and analyze. We offer a new service aimed to visualize and analyze the multiple alignments obtained with different external algorithms, with new features useful for the comparison of the aligned sequences as well as for the creation of a final image of the alignment. The service is named FASMA and is available at http://bioinformatica.isa.cnr.it/FASMA/.

Impact of guided exploration and enactive exploration on self-regulatory mechanisms and information acquisition through electronic search.

PubMed

Debowski, S; Wood, R E; Bandura, A

2001-12-01

Following instruction in basic skills for electronic search, participants who practiced in a guided exploration mode developed stronger self-efficacy and greater satisfaction than those who practiced in a self-guided exploratory mode. Intrinsic motivation was not affected by exploration mode. On 2 post-training tasks, guided exploration participants produced more effective search strategies. expended less effort, made fewer errors, rejected fewer lines of search, and achieved higher performance. Relative lack of support for self-regulatory factors as mediators of exploration mode impacts was attributed to the uninformative feedback from electronic search, which causes most people to remain at a novice level and to require external guidance for development of self-efficacy and skills. Self-guided learning will be more effective on structured tasks with more informative feedback and for individuals with greater expertise on dynamic tasks.

How Design Guides Learning from Matrix Diagrams

ERIC Educational Resources Information Center

van der Meij, Jan; van Amelsvoort, Marije; Anjewierden, Anjo

2017-01-01

Compared to text, diagrams are superior in their ability to structure and summarize information and to show relations between concepts and ideas. Perceptual cues, like arrows, are expected to improve the retention of diagrams by guiding the learner towards important elements or showing a preferred reading sequence. In our experiment, we analyzed…

Industrial Arts Curriculum Guide for Plastics.

ERIC Educational Resources Information Center

Connecticut State Dept. of Education, Hartford. Div. of Vocational Education.

This curriculum guide provides topic outlines and objectives for 12 units of an industrial arts program in plastics at any grade level. Introductory material describes the scope and sequence of an Industrial Arts program, gives specific guidelines for Industrial Arts, and briefly discusses the nature of plastics. Unit titles include Orientation of…

Dance: A Guide to Curriculum Development in the Arts.

ERIC Educational Resources Information Center

Iowa State Dept. of Public Instruction, Des Moines.

The purpose of this guide is to present dance education as a discipline and to encourage student participation in a wide range of dance activities. The unit, "Rationale/Philosophy/Goals," contains an introduction to the program, a rationale, and overall goals. "Scope/Sequence/Strategies," presents a chart which lists basic…

76 FR 39243 - Federal Acquisition Regulation; Federal Acquisition Circular 2005-53; Small Entity Compliance Guide

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-05

... ADMINISTRATION 48 CFR Chapter 1 [Docket FAR 2011-0077, Sequence 5] Federal Acquisition Regulation; Federal Acquisition Circular 2005-53; Small Entity Compliance Guide AGENCY: Department of Defense (DoD), General... Federal Acquisition Circular (FAC) 2005-53, which amend the Federal Acquisition Regulation (FAR). An...

Forestry Occupations. A Curriculum Guide.

ERIC Educational Resources Information Center

Mercer, R. J., Ed.

Developed as a part of a larger project to revise the total agricultural education curriculum in South Carolina, this curriculum guide is designed for a 2-year course in forestry occupations. A paradigm accompanies the document and illustrates a possible time frame and sequence. The units covered by the curriculum include an orientation to…

Industrial Arts Curriculum Guide for Electricity/Electronics.

ERIC Educational Resources Information Center

Connecticut State Dept. of Education, Hartford. Div. of Vocational Education.

This curriculum provides a behaviorally written guide that offers a possible list of objectives to assist in establishing or revising an electrical/electronics curriculum. Teachers may choose specific objectives to suit age group and educational level or expertise. Introductory material describes the scope and sequence of an Industrial Arts…

Industrial Technology Orientation Curriculum Guide.

ERIC Educational Resources Information Center

Illinois State Board of Education, Springfield. Dept. of Adult, Vocational and Technical Education.

The four courses in this guide were designed to meet the specifications for the career orientation level of Illinois' Education for Employment Curriculum Model. These orientation-level courses can be taken by high school students in any sequence: (1) communication technology; (2) energy utilization technology; (3) production technology; and (4)…

Elementary Art Education Guide.

ERIC Educational Resources Information Center

Frederick County Public Schools, MD.

This curriculum guide for elementary art education is divided into 21 parts. Following a preface and acknowledgements, the philosophy, framework, goals, and objectives of the art curriculum for Frederick County (Maryland) are outlined. Grade level course overviews and scope and sequence for art education in grades 1-5 are then presented. An…

A President's Guide to Fund-Raising Success: Relationships Are Key.

ERIC Educational Resources Information Center

Bornstein, Rita

2000-01-01

Stresses the importance of the relationship between the institution's president and its advancement vice president for successful college fund raising. Suggests that a successful external relations program requires expertise, loyalty, and reciprocity in this working relationship. (DB)

Otoplasty: sequencing the operation for improved results.

PubMed

Hoehn, James G; Ashruf, Salman

2005-01-01

: After studying this article, the participant should be able to: 1. Understand the anatomy and embryology of the external ear. 2. Understand the anatomic causes of the prominent ear. 3. Understand the operative maneuvers used to shape the external ear. 4. Be able to sequence the otoplasty for consistent results. 5. Understand the possible complications of the otoplasty procedure. Correction of prominent ears is a common plastic surgical procedure. Proper execution of the surgical techniques is dependent on the surgeon's understanding of the surgical procedure. This understanding is best founded on an understanding of the historical bases for the operative steps and the execution of these operative steps in a logical fashion. This article describes the concept of sequencing the operation of otoplasty to produce predictable results combining the technical contributions from many authors. The historical, embryological, and anatomic bases for the operation are also discussed. Finally, the authors' preferred techniques are presented. Sequencing the steps in the preoperative assessment, preoperative planning, patient management, operative technique, and postoperative care will produce reproducible results for the attentive surgeon. Careful attention to the details of the operation of otoplasty will avoid many postoperative problems.

Clinical application of fully digital Cerec surgical guides made in-house.

PubMed

Bindl, A

2015-01-01

It is now possible to produce full-digital drilling templates with Cerec Guide 2 (Sirona) in the dental practice relatively quickly, efficiently, and economically. Here, a patient case example is used to present an exemplary description of the procedure and method to do this. The solution described herein shows the advantageous efficiency, compared with other systems presently on the market, of a procedure that does not require the external production of the drilling template in the laboratory or a manufacturing center.

Variants of guided self-organization for robot control.

PubMed

Martius, Georg; Herrmann, J Michael

2012-09-01

Autonomous robots can generate exploratory behavior by self-organization of the sensorimotor loop. We show that the behavioral manifold that is covered in this way can be modified in a goal-dependent way without reducing the self-induced activity of the robot. We present three strategies for guided self-organization, namely by using external rewards, a problem-specific error function, or assumptions about the symmetries of the desired behavior. The strategies are analyzed for two different robots in a physically realistic simulation.

Experiences From Creating the Guide to the Systems Engineering Body of Knowledge (SEBoK) v. 1.0

DTIC Science & Technology

2013-03-01

00-00-2013 to 00-00-2013 4. TITLE AND SUBTITLE Experiences From Creating the Guide to the Systems Engineering Body of Knowledge (SEBoK) v. 1.0 5a...external sources, was not easy to achieve. SE Literature: The most comprehensive source of SE knowledge today is the Systems Engineering Handbook [3...recommended for further reading - SEBoK v. 1.0 includes 224 primary references; and (3) Additional references include other related literature that are good

Strongly magnetized classical plasma models

NASA Technical Reports Server (NTRS)

Montgomery, D. C.

1972-01-01

The class of plasma processes for which the so-called Vlasov approximation is inadequate is investigated. Results from the equilibrium statistical mechanics of two-dimensional plasmas are derived. These results are independent of the presence of an external dc magnetic field. The nonequilibrium statistical mechanics of the electrostatic guiding-center plasma, a two-dimensional plasma model, is discussed. This model is then generalized to three dimensions. The guiding-center model is relaxed to include finite Larmor radius effects for a two-dimensional plasma.

Navigation-guided optic canal decompression for traumatic optic neuropathy: Two case reports.

PubMed

Bhattacharjee, Kasturi; Serasiya, Samir; Kapoor, Deepika; Bhattacharjee, Harsha

2018-06-01

Two cases of traumatic optic neuropathy presented with profound loss of vision. Both cases received a course of intravenous corticosteroids elsewhere but did not improve. They underwent Navigation guided optic canal decompression via external transcaruncular approach, following which both cases showed visual improvement. Postoperative Visual Evoked Potential and optical coherence technology of Retinal nerve fibre layer showed improvement. These case reports emphasize on the role of stereotactic navigation technology for optic canal decompression in cases of traumatic optic neuropathy.

The bench scientist's guide to RNA-Seq analysis

USDA-ARS?s Scientific Manuscript database

RNA sequencing (RNA-Seq) is emerging as a highly accurate method to quantify transcript abundance. However, analyses of the large data sets obtained by sequencing the entire transcriptome of organisms have generally been performed by bioinformatic specialists. Here we outline a methods strategy desi...

Identification of the bacterial etiology of culture-negative endocarditis by amplification and sequencing of a small ribosomal RNA gene.

PubMed

Khulordava, Irakli; Miller, Geraldine; Haas, David; Li, Haijing; McKinsey, Joel; Vanderende, Daniel; Tang, Yi-Wei

2003-05-01

We report two cases of culture-negative bacterial endocarditis in which the organisms were identified by amplification and sequencing of the bacterial 16S rRNA gene. These results support an important role for polymerase chain reaction followed by direct sequencing to determine the etiology of culture-negative bacterial endocarditis and to guide appropriate antimicrobial therapy.

Mechanism of anion permeation through the muscle fibre membrane of an elasmobranch fish, Taeniura lymma.

PubMed

Hagiwara, S; Takahashi, K

1974-04-01

1. Properties of anion permeation through the membrane of skeletal muscle fibres of the stingray, Taeniura lymma, were studied with intracellular recording and polarization techniques.2. The Cl conductance of the resting membrane in the normal stingray saline at pH 7.7 is 8-10 times greater than the K conductance.3. The Cl conductance decreases with decreasing external pH, with an apparent pK of 5.3, whereas the K conductance is independent of pH between 4 and 9.4. The Q(10) of the Cl conductance is about 2.0, compared with a value of 1.2-1.4 for the K conductance.5. The Cl conductance is proportional to the external Cl concentration when observed after the fibre is equilibrated in the test solution.6. The permeability sequence obtained by potential measurement is SCN > NO(3) > Cl = Br > I > ClO(3) and the permeability ratio is independent of the mole fraction of anions.7. The conductance sequence determined by total replacement of the external Cl with other anion species differs from the permeability sequence and the conductance observed for partial replacement deviates significantly from that expected from the independence principle.8. Possible mechanisms of anion permeation are discussed.

Mechanism of anion permeation through the muscle fibre membrane of an elasmobranch fish, Taeniura lymma

PubMed Central

Hagiwara, Susumu; Takahashi, Kunitaro

1974-01-01

1. Properties of anion permeation through the membrane of skeletal muscle fibres of the stingray, Taeniura lymma, were studied with intracellular recording and polarization techniques. 2. The Cl conductance of the resting membrane in the normal stingray saline at pH 7·7 is 8-10 times greater than the K conductance. 3. The Cl conductance decreases with decreasing external pH, with an apparent pK of 5·3, whereas the K conductance is independent of pH between 4 and 9. 4. The Q10 of the Cl conductance is about 2·0, compared with a value of 1·2-1·4 for the K conductance. 5. The Cl conductance is proportional to the external Cl concentration when observed after the fibre is equilibrated in the test solution. 6. The permeability sequence obtained by potential measurement is SCN > NO3 > Cl = Br > I > ClO3 and the permeability ratio is independent of the mole fraction of anions. 7. The conductance sequence determined by total replacement of the external Cl with other anion species differs from the permeability sequence and the conductance observed for partial replacement deviates significantly from that expected from the independence principle. 8. Possible mechanisms of anion permeation are discussed. PMID:4838800

Metagenomic Taxonomy-Guided Database-Searching Strategy for Improving Metaproteomic Analysis.

PubMed

Xiao, Jinqiu; Tanca, Alessandro; Jia, Ben; Yang, Runqing; Wang, Bo; Zhang, Yu; Li, Jing

2018-04-06

Metaproteomics provides a direct measure of the functional information by investigating all proteins expressed by a microbiota. However, due to the complexity and heterogeneity of microbial communities, it is very hard to construct a sequence database suitable for a metaproteomic study. Using a public database, researchers might not be able to identify proteins from poorly characterized microbial species, while a sequencing-based metagenomic database may not provide adequate coverage for all potentially expressed protein sequences. To address this challenge, we propose a metagenomic taxonomy-guided database-search strategy (MT), in which a merged database is employed, consisting of both taxonomy-guided reference protein sequences from public databases and proteins from metagenome assembly. By applying our MT strategy to a mock microbial mixture, about two times as many peptides were detected as with the metagenomic database only. According to the evaluation of the reliability of taxonomic attribution, the rate of misassignments was comparable to that obtained using an a priori matched database. We also evaluated the MT strategy with a human gut microbial sample, and we found 1.7 times as many peptides as using a standard metagenomic database. In conclusion, our MT strategy allows the construction of databases able to provide high sensitivity and precision in peptide identification in metaproteomic studies, enabling the detection of proteins from poorly characterized species within the microbiota.

Preoperative localization of intracranial lesions with MRI using marking pills.

PubMed

Shibata, Sumiya; Kunieda, Takeharu; Adachi, Hidemitsu; Ueno, Yasushi; Kohara, Nobuo; Sakai, Nobuyuki

2011-12-01

To describe a simple technique for preoperative surface localization of intracranial lesions. 11 pills in total, including Alfarol (alfacalcidol) capsules, were affixed to a phantom with adhesive tape and a MRI scan was performed. The visibility of the pills and any spatial errors in determining their locations were evaluated. Between June 2006 and April 2009, we employed Alfarol capsules as a skin marker in MRI in clinical surgical cases. Alfarol capsules, whose actual size is 5.6 mm in diameter, were identified as a hyperintense spot at a size of 4.2, 4.2, and 4.5mm in diameter in T1-weighted, T2-weighted, and FLAIR (fluid attenuated inversion recovery) sequence images, respectively. The size discrepancies were within 1.4 mm. The average spatial errors were 0.7, 0.6, and 0.7 mm in T1-weighted, T2-weighted, and FLAIR sequence images, respectively. Other pills were not identified in the MRI scans. During this 35-month period, 8 patients underwent preoperative MRI-guided localization at our institution. There were 5 men and 3 women in whom 8 biopsies were performed. In all cases, the result of the biopsy was positive and useful for the treatment that followed. No perioperative complications were encountered. Alfarol capsule can be used as an external skin marker. Our simple and inexpensive method is a useful addition to preoperative evaluation of superficial intracranial lesions. Copyright © 2011 Elsevier B.V. All rights reserved.

Simultaneous phylogeny reconstruction and multiple sequence alignment

PubMed Central

Yue, Feng; Shi, Jian; Tang, Jijun

2009-01-01

Background A phylogeny is the evolutionary history of a group of organisms. To date, sequence data is still the most used data type for phylogenetic reconstruction. Before any sequences can be used for phylogeny reconstruction, they must be aligned, and the quality of the multiple sequence alignment has been shown to affect the quality of the inferred phylogeny. At the same time, all the current multiple sequence alignment programs use a guide tree to produce the alignment and experiments showed that good guide trees can significantly improve the multiple alignment quality. Results We devise a new algorithm to simultaneously align multiple sequences and search for the phylogenetic tree that leads to the best alignment. We also implemented the algorithm as a C program package, which can handle both DNA and protein data and can take simple cost model as well as complex substitution matrices, such as PAM250 or BLOSUM62. The performance of the new method are compared with those from other popular multiple sequence alignment tools, including the widely used programs such as ClustalW and T-Coffee. Experimental results suggest that this method has good performance in terms of both phylogeny accuracy and alignment quality. Conclusion We present an algorithm to align multiple sequences and reconstruct the phylogenies that minimize the alignment score, which is based on an efficient algorithm to solve the median problems for three sequences. Our extensive experiments suggest that this method is very promising and can produce high quality phylogenies and alignments. PMID:19208110

Practice-Based Evidence in Community Guide Systematic Reviews.

PubMed

Vaidya, Namita; Thota, Anilkrishna B; Proia, Krista K; Jamieson, Sara; Mercer, Shawna L; Elder, Randy W; Yoon, Paula; Kaufmann, Rachel; Zaza, Stephanie

2017-03-01

To assess the relative contributions and quality of practice-based evidence (PBE) and research-based evidence (RBE) in The Guide to Community Preventive Services (The Community Guide). We developed operational definitions for PBE and RBE in which the main distinguishing feature was whether allocation of participants to intervention and comparison conditions was under the control of researchers (RBE) or not (PBE). We conceptualized a continuum between RBE and PBE. We then categorized 3656 studies in 202 reviews completed since The Community Guide began in 1996. Fifty-four percent of studies were PBE and 46% RBE. Community-based and policy reviews had more PBE. Health care system and programmatic reviews had more RBE. The majority of both PBE and RBE studies were of high quality according to Community Guide scoring methods. The inclusion of substantial PBE in Community Guide reviews suggests that evidence of adequate rigor to inform practice is being produced. This should increase stakeholders' confidence that The Community Guide provides recommendations with real-world relevance. Limitations in some PBE studies suggest a need for strengthening practice-relevant designs and external validity reporting standards.

An approach for identification of unknown viruses using sequencing-by-hybridization.

PubMed

Katoski, Sarah E; Meyer, Hermann; Ibrahim, Sofi

2015-09-01

Accurate identification of biological threat agents, especially RNA viruses, in clinical or environmental samples can be challenging because the concentration of viral genomic material in a given sample is usually low, viral genomic RNA is liable to degradation, and RNA viruses are extremely diverse. A two-tiered approach was used for initial identification, then full genomic characterization of 199 RNA viruses belonging to virus families Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, and Togaviridae. A Sequencing-by-hybridization (SBH) microarray was used to tentatively identify a viral pathogen then, the identity is confirmed by guided next-generation sequencing (NGS). After optimization and evaluation of the SBH and NGS methodologies with various virus species and strains, the approach was used to test the ability to identify viruses in blinded samples. The SBH correctly identified two Ebola viruses in the blinded samples within 24 hr, and by using guided amplicon sequencing with 454 GS FLX, the identities of the viruses in both samples were confirmed. SBH provides at relatively low-cost screening of biological samples against a panel of viral pathogens that can be custom-designed on a microarray. Once the identity of virus is deduced from the highest hybridization signal on the SBH microarray, guided (amplicon) NGS sequencing can be used not only to confirm the identity of the virus but also to provide further information about the strain or isolate, including a potential genetic manipulation. This approach can be useful in situations where natural or deliberate biological threat incidents might occur and a rapid response is required. © 2015 Wiley Periodicals, Inc.

A global view of structure–function relationships in the tautomerase superfamily

PubMed Central

Davidson, Rebecca; Baas, Bert-Jan; Akiva, Eyal; Holliday, Gemma L.; Polacco, Benjamin J.; LeVieux, Jake A.; Pullara, Collin R.; Zhang, Yan Jessie; Whitman, Christian P.

2018-01-01

The tautomerase superfamily (TSF) consists of more than 11,000 nonredundant sequences present throughout the biosphere. Characterized members have attracted much attention because of the unusual and key catalytic role of an N-terminal proline. These few characterized members catalyze a diverse range of chemical reactions, but the full scale of their chemical capabilities and biological functions remains unknown. To gain new insight into TSF structure–function relationships, we performed a global analysis of similarities across the entire superfamily and computed a sequence similarity network to guide classification into distinct subgroups. Our results indicate that TSF members are found in all domains of life, with most being present in bacteria. The eukaryotic members of the cis-3-chloroacrylic acid dehalogenase subgroup are limited to fungal species, whereas the macrophage migration inhibitory factor subgroup has wide eukaryotic representation (including mammals). Unexpectedly, we found that 346 TSF sequences lack Pro-1, of which 85% are present in the malonate semialdehyde decarboxylase subgroup. The computed network also enabled the identification of similarity paths, namely sequences that link functionally diverse subgroups and exhibit transitional structural features that may help explain reaction divergence. A structure-guided comparison of these linker proteins identified conserved transitions between them, and kinetic analysis paralleled these observations. Phylogenetic reconstruction of the linker set was consistent with these findings. Our results also suggest that contemporary TSF members may have evolved from a short 4-oxalocrotonate tautomerase–like ancestor followed by gene duplication and fusion. Our new linker-guided strategy can be used to enrich the discovery of sequence/structure/function transitions in other enzyme superfamilies. PMID:29184004

GA-based fuzzy reinforcement learning for control of a magnetic bearing system.

PubMed

Lin, C T; Jou, C P

2000-01-01

This paper proposes a TD (temporal difference) and GA (genetic algorithm)-based reinforcement (TDGAR) learning method and applies it to the control of a real magnetic bearing system. The TDGAR learning scheme is a new hybrid GA, which integrates the TD prediction method and the GA to perform the reinforcement learning task. The TDGAR learning system is composed of two integrated feedforward networks. One neural network acts as a critic network to guide the learning of the other network (the action network) which determines the outputs (actions) of the TDGAR learning system. The action network can be a normal neural network or a neural fuzzy network. Using the TD prediction method, the critic network can predict the external reinforcement signal and provide a more informative internal reinforcement signal to the action network. The action network uses the GA to adapt itself according to the internal reinforcement signal. The key concept of the TDGAR learning scheme is to formulate the internal reinforcement signal as the fitness function for the GA such that the GA can evaluate the candidate solutions (chromosomes) regularly, even during periods without external feedback from the environment. This enables the GA to proceed to new generations regularly without waiting for the arrival of the external reinforcement signal. This can usually accelerate the GA learning since a reinforcement signal may only be available at a time long after a sequence of actions has occurred in the reinforcement learning problem. The proposed TDGAR learning system has been used to control an active magnetic bearing (AMB) system in practice. A systematic design procedure is developed to achieve successful integration of all the subsystems including magnetic suspension, mechanical structure, and controller training. The results show that the TDGAR learning scheme can successfully find a neural controller or a neural fuzzy controller for a self-designed magnetic bearing system.

RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome

USDA-ARS?s Scientific Manuscript database

A first analysis of the Glycine max (L.) Merr. (soybean) transcriptome using next generation sequencing technology and RNA-Sequencing (RNA-Seq) is presented. This analysis will provide an important resource for understanding transcription and gene co-regulatory networks in soybean, the most economic...

Single-cell genomic sequencing using Multiple Displacement Amplification.

PubMed

Lasken, Roger S

2007-10-01

Single microbial cells can now be sequenced using DNA amplified by the Multiple Displacement Amplification (MDA) reaction. The few femtograms of DNA in a bacterium are amplified into micrograms of high molecular weight DNA suitable for DNA library construction and Sanger sequencing. The MDA-generated DNA also performs well when used directly as template for pyrosequencing by the 454 Life Sciences method. While MDA from single cells loses some of the genomic sequence, this approach will greatly accelerate the pace of sequencing from uncultured microbes. The genetically linked sequences from single cells are also a powerful tool to be used in guiding genomic assembly of shotgun sequences of multiple organisms from environmental DNA extracts (metagenomic sequences).

Orthodontic-periodontal interactions: Orthodontic extrusion in interdisciplinary regenerative treatments.

PubMed

Paolone, Maria Giacinta; Kaitsas, Roberto

2018-06-01

Orthodontics is a periodontal treatment. "Guided orthodontic regeneration" (GOR) procedures use orthodontic movements in perio-restorative patients. The GOR technique includes a guided orthodontic "soft tissue" regeneration (GOTR) and a guided orthodontic "bone" regeneration (GOBR) with a plastic soft tissue approach and a regenerating reality. The increased amount of soft tissue gained with orthodontic movement can be used for subsequent periodontal regenerative techniques. The increased amount of bone can as well improve primary implant stability and, eventually, simplify a GTR technique to regenerate soft tissues, to restore tooth with external resorption in aesthetic zone or to extract a tooth to create new hard-soft tissue for adjacent teeth. Copyright © 2018. Published by Elsevier Masson SAS.

Diversity and Periodicity: An Inorganic Chemistry Module. Teacher's Guide.

ERIC Educational Resources Information Center

Huheey, James; Sandoval, Amado

This teacher's guide is designed to provide science teachers with the necessary guidance and suggestions for teaching inorganic chemistry. The material in this book can be integrated with the other modules in a sequence that helps students to see that chemistry is a unified science. Contents include: (1) "Periodicity: A Chemical Calendar"; (2)…

Communities of Molecules: A Physical Chemistry Module. Teacher's Guide.

ERIC Educational Resources Information Center

DeVoe, Howard; Hearle, Robert

This teacher's guide is designed to provide science teachers with the necessary guidance and suggestions for teaching physical chemistry. The material in this book can be integrated with the other modules in a sequence that helps students see that chemistry is a unified science. Contents include: (1) "Introduction of Physical Chemistry"; (2) "The…

Farm Crops: Unit Manual Eleven. Curriculum Guide.

ERIC Educational Resources Information Center

Lewis, Ann; And Others

This is number 11 in a series of resource manuals consisting of 11 sequenced curriculum guides developed by the Demonstration and Research Center for Early Education (DARCEE) for use in early childhood education programs. Emphasis is placed on the development of sensory, abstracting and mediating, and response skills. The projected order of the…

Business Economics: Task Analyses. Competency-Based Education.

ERIC Educational Resources Information Center

Henrico County Public Schools, Glen Allen, VA. Virginia Vocational Curriculum Center.

This task analyses guide is designed to be used in combination with the "Business Education Service Area Resource" in order to implement competency-based education in the Business Economics course in Virginia. The task analyses guide contains the task inventory, suggested task sequence list, and content outline for the specific course in business…

Resources for Teaching HERO: Food Service Occupations in Montana.

ERIC Educational Resources Information Center

Parsons, Angelina O.; Harris, Pamela R.

This resource guide is designed to help home economics teachers in Montana to develop occupational programs for food service. It provides resources that can be used with the "Food Service Occupations in Montana: Scope and Sequence in Wage-Earning Home Economics." The guide contains 13 sections. The first section explains the core…

Air University Suggested Professional Reading Guide.

ERIC Educational Resources Information Center

Air Univ., Maxwell AFB, AL.

One of six related documents intended for the Air Force officer, the enlisted man, or the civilian, this reading guide contains an annotated list of 26 publications that support Project Warrior and provide information about military history and the Air Force heritage. The books are listed in sequence according to a reading ease index, which…

Health Education Guide: A Design for Teaching K-12.

ERIC Educational Resources Information Center

Barrett, Morris

This teaching guide to health education includes instruction units for grades K-12. Section 1 discusses the need for health education and includes a scope and sequence chart for each of the instruction units. Section 2 consists of instruction units in the areas of physical development, social and emotional development, chemicals and addiction, and…

Consumer Education: A Senior High Elective Course.

ERIC Educational Resources Information Center

Grout, Marjorie; Rozell, Anthony

The overall objective of this elective senior course and guide is to lead the non-college-bound student toward the maturity of consumer judgement necessary in the complex economic marketplace of today. The scope and sequence section of this guide lists the eight units and includes basic objectives, and conceptual understandings for each: 1)…

Using Cinematic Techniques in a Multimedia Museum Guide.

ERIC Educational Resources Information Center

Zancanaro, M.; Stock, O.; Alfaro, I.

This paper introduces the idea of enhancing the audio presentation of a multimedia museum guide by using the PDA screen to travel throughout a fresco and identify the various details in it. During the presentation, a sequence of pictures is synchronized with the audio commentary, and the transitions among the pictures are planned according to…

Social Studies Program Guide, 9-12: The Senior High School.

ERIC Educational Resources Information Center

Spokane School District 81, WA.

This is the last of four guides which identify the scope, sequence, goals, and resources for the social studies program of the Spokane public schools. It suggests materials, resources, and activities related to social studies knowledge and skill development for grades 9 through 12. Lessons on all social science disciplines are outlined with…

High School Industrial Arts. A Guide for Teachers.

ERIC Educational Resources Information Center

Oregon State Dept. of Education, Salem.

This teacher's guide is designed to help high school industrial arts teachers plan activities to develop their students' awareness of technology in our culture and the variety of related careers available to them. Discussed first are the objectives, scope, and sequence of industrial arts. Next, the special characteristics and needs of adolescents,…

A Planning Guide for Gifted Preschoolers.

ERIC Educational Resources Information Center

Malley-Crist, Justine; And Others

Contained in the curriculum planning guide developed by the Chapel Hill Gifted-Handicapped Project are a model, a training sequence, and 17 instructional units for use with preschool gifted children. The model is explained to be based on the hierarchy of cognitive tasks developed by B. Bloom. A worksheet for teachers suggests activities to help…

Western Civilization Curriculum Guide. Bulletin 1759.

ERIC Educational Resources Information Center

Louisiana State Dept. of Education, Baton Rouge. Div. of Academic Programs.

Developed to stress the importance of the study of Western civilization, this Louisiana State high school curriculum guide contains social studies goals, program scopes and sequences, a list of 14 generalizations and related concepts, and a master course content outline. Ten study units teach about: (1) the ancient world; (2) the Middle Ages; (3)…

Using Literature-Based Prompts To Teach Writing Competencies: Directed Reading and Writing Lessons.

ERIC Educational Resources Information Center

Gelsinger, Barry D.

Intended to help teachers integrate writing instruction with the study of literature, this teaching guide offers a philosophy of writing instruction, describes a procedure for teaching reading and writing lessons, and provides a sequence of writing skills. For various literature selections, the guide defines vocabulary, provides topic discussion…

World History Curriculum Guide: Secondary Social Studies. Bulletin 1758.

ERIC Educational Resources Information Center

Louisiana State Dept. of Education, Baton Rouge. Div. of Academic Programs.

This state curriculum guide was developed to reaffirm the importance of world history in the Louisiana social studies curriculum. It contains statements of the Louisiana social studies goals, program scopes and sequences, a list of 14 generalizations and related concepts, and a master course content outline. Seven study units are presented that…

Creativity: A Saleable Work Skill. Occupation Simulation Packet. Grades 3rd-4th.

ERIC Educational Resources Information Center

Dye, Dick

This teacher's guide for grades 3 and 4 contains simulated work experiences for students using the isolated skill concept - creativity. Teacher instructions include objectives, evaluation, and sequence of activities. The guide contains pre-tests and post-tests with instructions and answer keys. Two pre-skill activities are suggested, such as…

Base pairing between the 3' exon and an internal guide sequence increases 3' splice site specificity in the Tetrahymena self-splicing rRNA intron.

PubMed Central

Suh, E R; Waring, R B

1990-01-01

It has been proposed that recognition of the 3' splice site in many group I introns involves base pairing between the start of the 3' exon and a region of the intron known as the internal guide sequence (R. W. Davies, R. B. Waring, J. Ray, T. A. Brown, and C. Scazzocchio, Nature [London] 300:719-724, 1982). We have examined this hypothesis, using the self-splicing rRNA intron from Tetrahymena thermophila. Mutations in the 3' exon that weaken this proposed pairing increased use of a downstream cryptic 3' splice site. Compensatory mutations in the guide sequence that restore this pairing resulted in even stronger selection of the normal 3' splice site. These changes in 3' splice site usage were more pronounced in the background of a mutation (414A) which resulted in an adenine instead of a guanine being the last base of the intron. These results show that the proposed pairing (P10) plays an important role in ensuring that cryptic 3' splice sites are selected against. Surprisingly, the 414A mutation alone did not result in activation of the cryptic 3' splice site. Images PMID:2342465

Protospacer Adjacent Motif (PAM)-Distal Sequences Engage CRISPR Cas9 DNA Target Cleavage

PubMed Central

Ethier, Sylvain; Schmeing, T. Martin; Dostie, Josée; Pelletier, Jerry

2014-01-01

The clustered regularly interspaced short palindromic repeat (CRISPR)-associated enzyme Cas9 is an RNA-guided nuclease that has been widely adapted for genome editing in eukaryotic cells. However, the in vivo target specificity of Cas9 is poorly understood and most studies rely on in silico predictions to define the potential off-target editing spectrum. Using chromatin immunoprecipitation followed by sequencing (ChIP-seq), we delineate the genome-wide binding panorama of catalytically inactive Cas9 directed by two different single guide (sg) RNAs targeting the Trp53 locus. Cas9:sgRNA complexes are able to load onto multiple sites with short seed regions adjacent to 5′NGG3′ protospacer adjacent motifs (PAM). Yet among 43 ChIP-seq sites harboring seed regions analyzed for mutational status, we find editing only at the intended on-target locus and one off-target site. In vitro analysis of target site recognition revealed that interactions between the 5′ end of the guide and PAM-distal target sequences are necessary to efficiently engage Cas9 nucleolytic activity, providing an explanation for why off-target editing is significantly lower than expected from ChIP-seq data. PMID:25275497

Diminished neural responses predict enhanced intrinsic motivation and sensitivity to external incentive.

PubMed

Marsden, Karen E; Ma, Wei Ji; Deci, Edward L; Ryan, Richard M; Chiu, Pearl H

2015-06-01

The duration and quality of human performance depend on both intrinsic motivation and external incentives. However, little is known about the neuroscientific basis of this interplay between internal and external motivators. Here, we used functional magnetic resonance imaging to examine the neural substrates of intrinsic motivation, operationalized as the free-choice time spent on a task when this was not required, and tested the neural and behavioral effects of external reward on intrinsic motivation. We found that increased duration of free-choice time was predicted by generally diminished neural responses in regions associated with cognitive and affective regulation. By comparison, the possibility of additional reward improved task accuracy, and specifically increased neural and behavioral responses following errors. Those individuals with the smallest neural responses associated with intrinsic motivation exhibited the greatest error-related neural enhancement under the external contingency of possible reward. Together, these data suggest that human performance is guided by a "tonic" and "phasic" relationship between the neural substrates of intrinsic motivation (tonic) and the impact of external incentives (phasic).

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9.

PubMed

Sternberg, Samuel H; Redding, Sy; Jinek, Martin; Greene, Eric C; Doudna, Jennifer A

2014-03-06

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA-DNA base-pairing to target foreign DNA in bacteria. Cas9-guide RNA complexes are also effective genome engineering agents in animals and plants. Here we use single-molecule and bulk biochemical experiments to determine how Cas9-RNA interrogates DNA to find specific cleavage sites. We show that both binding and cleavage of DNA by Cas9-RNA require recognition of a short trinucleotide protospacer adjacent motif (PAM). Non-target DNA binding affinity scales with PAM density, and sequences fully complementary to the guide RNA but lacking a nearby PAM are ignored by Cas9-RNA. Competition assays provide evidence that DNA strand separation and RNA-DNA heteroduplex formation initiate at the PAM and proceed directionally towards the distal end of the target sequence. Furthermore, PAM interactions trigger Cas9 catalytic activity. These results reveal how Cas9 uses PAM recognition to quickly identify potential target sites while scanning large DNA molecules, and to regulate scission of double-stranded DNA.

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

NASA Astrophysics Data System (ADS)

Sternberg, Samuel H.; Redding, Sy; Jinek, Martin; Greene, Eric C.; Doudna, Jennifer A.

2014-03-01

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA-DNA base-pairing to target foreign DNA in bacteria. Cas9-guide RNA complexes are also effective genome engineering agents in animals and plants. Here we use single-molecule and bulk biochemical experiments to determine how Cas9-RNA interrogates DNA to find specific cleavage sites. We show that both binding and cleavage of DNA by Cas9-RNA require recognition of a short trinucleotide protospacer adjacent motif (PAM). Non-target DNA binding affinity scales with PAM density, and sequences fully complementary to the guide RNA but lacking a nearby PAM are ignored by Cas9-RNA. Competition assays provide evidence that DNA strand separation and RNA-DNA heteroduplex formation initiate at the PAM and proceed directionally towards the distal end of the target sequence. Furthermore, PAM interactions trigger Cas9 catalytic activity. These results reveal how Cas9 uses PAM recognition to quickly identify potential target sites while scanning large DNA molecules, and to regulate scission of double-stranded DNA.

Ultrasound guided transarterial coil placement in the internal and external carotid artery in horses.

PubMed

Muñoz, Juan; Iglesias, Manuel; Chao, Eduardo Lloret; Bussy, Christian

2015-04-01

To assess ultrasound guided transarterial coil placement (UGTACP) for occlusion of the internal carotid artery (ICA) and external carotid artery (ECA) in horses. Cadaveric and in vivo study. Cadaveric horses (n = 10), healthy horses (3), and 1 clinical case. Cadaveric and in vivo (healthy horses): UGTACP was performed in the caudal part of the ICA and ECA. Coil placement in the rostral part of the ICA was performed blindly and controlled by conventional radiography. No coils were placed in the rostral part of the ECA. UGTACP of the ICA was in a horse with guttural pouch mycosis of the left guttural pouch. Accurate ultrasound-guided catheterization of the ICA and ECA was performed in all specimens. Ultrasound-guided coil placement was successfully performed in all cases except 1. No complications occurred in the in vivo study. The clinical case fully recovered and returned to its intended use. Based on our study, UGTACP of the ICA and ECA caudal part is a feasible alternative to fluoroscopy. An advantage of this technique is the accuracy with which you can catheterize both ICA and ECA and the ability to identify unusual branching at the origin of the ICA. Regarding the rostral part of the ICA, angiographic catheter guidance in this region is probably more precise using fluoroscopy as it is performed blindly. In a clinical situation, combination of US and fluoroscopy guidance can result in reduction of radiation exposure time. © Copyright 2014 by The American College of Veterinary Surgeons.

Impacts of crop sequence and minimum and no-till cropping systems on soil carbon stocks in south-central North Dakota, USA

USDA-ARS?s Scientific Manuscript database

Increased emphasis has been placed on developing agroecosystems that are inherently resistant and resilient to external stressors, yet are highly productive, economically competitive, and environmentally benign. As part of a long-term study to evaluate effects of crop sequence and tillage on crop yi...

Health-related external cost assessment in Europe: methodological developments from ExternE to the 2013 Clean Air Policy Package.

PubMed

van der Kamp, Jonathan; Bachmann, Till M

2015-03-03

"Getting the prices right" through internalizing external costs is a guiding principle of environmental policy making, one recent example being the EU Clean Air Policy Package released at the end of 2013. It is supported by impact assessments, including monetary valuation of environmental and health damages. For over 20 years, related methodologies have been developed in Europe in the Externalities of Energy (ExternE) project series and follow-up activities. In this study, we aim at analyzing the main methodological developments over time from the 1990s until today with a focus on classical air pollution-induced human health damage costs. An up-to-date assessment including the latest European recommendations is also applied. Using a case from the energy sector, we identify major influencing parameters: differences in exposure modeling and related data lead to variations in damage costs of up to 21%; concerning risk assessment and monetary valuation, differences in assessing long-term exposure mortality risks together with assumptions on particle toxicity explain most of the observed changes in damage costs. These still debated influencing parameters deserve particular attention when damage costs are used to support environmental policy making.

External Contamination Control of Attached Payloads on the International Space Station

NASA Technical Reports Server (NTRS)

Soares, Carlos E.; Mikatarian, Ronald R.; Olsen, Randy L.; Huang, Alvin Y.; Steagall, Courtney A.; Schmidl, William D.; Wright, Bruce D.; Koontz, Steven

2012-01-01

The International Space Station (ISS) is an on-orbit platform for science utilization in low Earth orbit with multiple sites for external payloads with exposure to the natural and induced environments. Contamination is one of the induced environments that can impact performance, mission success and science utilization on the vehicle. This paper describes the external contamination control requirements and integration process for externally mounted payloads on the ISS. The external contamination control requirements are summarized and a description of the integration and verification process is detailed to guide payload developers in the certification process of attached payloads on the vehicle. A description of the required data certification deliverables covers the characterization of contamination sources. Such characterization includes identification, usage and operational data for each class of contamination source. Classes of external contamination sources covered are vacuum exposed materials, sources of leakage, vacuum venting and thrusters. ISS system level analyses are conducted by the ISS Space Environments Team to certify compliance with external contamination control requirements. This paper also addresses the ISS induced contamination environment at attached payload sites, both at the requirements level as well as measurements made on ISS.

Accelerated radiation damping for increased spin equilibrium (ARISE): a new method for controlling the recovery of longitudinal magnetization.

PubMed

Huang, Susie Y; Witzel, Thomas; Wald, Lawrence L

2008-11-01

Control of the longitudinal magnetization in fast gradient-echo (GRE) sequences is an important factor in enabling the high efficiency of balanced steady-state free precession (bSSFP) sequences. We introduce a new method for accelerating the return of the longitudinal magnetization to the +z-axis that is independent of externally applied RF pulses and shows improved off-resonance performance. The accelerated radiation damping for increased spin equilibrium (ARISE) method uses an external feedback circuit to strengthen the radiation damping (RD) field. The enhanced RD field rotates the magnetization back to the +z-axis at a rate faster than T(1) relaxation. The method is characterized in GRE phantom imaging at 3T as a function of feedback gain, phase, and duration, and compared with results from numerical simulations of the Bloch equations incorporating RD. A short period of feedback (10 ms) during a refocused interval of a crushed GRE sequence allowed greater than 99% recovery of the longitudinal magnetization when very little T(2) relaxation had time to occur. An appropriate application might be to improve navigated sequences. Unlike conventional flip-back schemes, the ARISE "flip-back" is generated by the spins themselves, thereby offering a potentially useful building block for enhancing GRE sequences.

The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects.

PubMed

Kamola, Piotr J; Nakano, Yuko; Takahashi, Tomoko; Wilson, Paul A; Ui-Tei, Kumiko

2015-12-01

RNA interference (RNAi) is a powerful tool for post-transcriptional gene silencing. However, the siRNA guide strand may bind unintended off-target transcripts via partial sequence complementarity by a mechanism closely mirroring micro RNA (miRNA) silencing. To better understand these off-target effects, we investigated the correlation between sequence features within various subsections of siRNA guide strands, and its corresponding target sequences, with off-target activities. Our results confirm previous reports that strength of base-pairing in the siRNA seed region is the primary factor determining the efficiency of off-target silencing. However, the degree of downregulation of off-target transcripts with shared seed sequence is not necessarily similar, suggesting that there are additional auxiliary factors that influence the silencing potential. Here, we demonstrate that both the melting temperature (Tm) in a subsection of siRNA non-seed region, and the GC contents of its corresponding target sequences, are negatively correlated with the efficiency of off-target effect. Analysis of experimentally validated miRNA targets demonstrated a similar trend, indicating a putative conserved mechanistic feature of seed region-dependent targeting mechanism. These observations may prove useful as parameters for off-target prediction algorithms and improve siRNA 'specificity' design rules.

A field ornithologist’s guide to genomics: Practical considerations for ecology and conservation

USGS Publications Warehouse

Oyler-McCance, Sara J.; Oh, Kevin; Langin, Kathryn; Aldridge, Cameron L.

2016-01-01

Vast improvements in sequencing technology have made it practical to simultaneously sequence millions of nucleotides distributed across the genome, opening the door for genomic studies in virtually any species. Ornithological research stands to benefit in three substantial ways. First, genomic methods enhance our ability to parse and simultaneously analyze both neutral and non-neutral genomic regions, thus providing insight into adaptive evolution and divergence. Second, the sheer quantity of sequence data generated by current sequencing platforms allows increased precision and resolution in analyses. Third, high-throughput sequencing can benefit applications that focus on a small number of loci that are otherwise prohibitively expensive, time-consuming, and technically difficult using traditional sequencing methods. These advances have improved our ability to understand evolutionary processes like speciation and local adaptation, but they also offer many practical applications in the fields of population ecology, migration tracking, conservation planning, diet analyses, and disease ecology. This review provides a guide for field ornithologists interested in incorporating genomic approaches into their research program, with an emphasis on techniques related to ecology and conservation. We present a general overview of contemporary genomic approaches and methods, as well as important considerations when selecting a genomic technique. We also discuss research questions that are likely to benefit from utilizing high-throughput sequencing instruments, highlighting select examples from recent avian studies.

Brushed permanent magnet DC MLC motor operation in an external magnetic field.

PubMed

Yun, J; St Aubin, J; Rathee, S; Fallone, B G

2010-05-01

Linac-MR systems for real-time image-guided radiotherapy will utilize the multileaf collimators (MLCs) to perform conformal radiotherapy and tumor tracking. The MLCs would be exposed to the external fringe magnetic fields of the linac-MR hybrid systems. Therefore, an experimental investigation of the effect of an external magnetic field on the brushed permanent magnet DC motors used in some MLC systems was performed. The changes in motor speed and current were measured for varying external magnetic field strengths up to 2000 G generated by an EEV electromagnet. These changes in motor characteristics were measured for three orientations of the motor in the external magnetic field, mimicking changes in motor orientations due to installation and/or collimator rotations. In addition, the functionality of the associated magnetic motor encoder was tested. The tested motors are used with the Varian 120 leaf Millennium MLC (Maxon Motor half leaf and full leaf motors) and the Varian 52 leaf MKII MLC (MicroMo Electronics leaf motor) including a carriage motor (MicroMo Electronics). In most cases, the magnetic encoder of the motors failed prior to any damage to the gearbox or the permanent magnet motor itself. This sets an upper limit of the external magnetic field strength on the motor function. The measured limits of the external magnetic fields were found to vary by the motor type. The leaf motor used with a Varian 52 leaf MKII MLC system tolerated up to 450 +/- 10 G. The carriage motor tolerated up to 2000 +/- 10 G field. The motors used with the Varian 120 leaf Millennium MLC system were found to tolerate a maximum of 600 +/- 10 G. The current Varian MLC system motors can be used for real-time image-guided radiotherapy coupled to a linac-MR system, provided the fringe magnetic fields at their locations are below the determined tolerance levels. With the fringe magnetic fields of linac-MR systems expected to be larger than the tolerance levels determined, some form of magnetic shielding would be required.

Dual mode fuel injector with one piece needle valve member

DOEpatents

Lawrence, Keith E.; Hinrichsen, Michael H.; Buckman, Colby

2005-01-18

A fuel injector includes a homogenous charge nozzle outlet set and a conventional nozzle outlet set controlled respectively by inner and outer needle value members. The homogenous charged nozzle outlet set is defined by an outer needle value member that is moveably positioned in an injector body, which defines the conventional nozzle outlet set. The inner needle valve member is positioned in the outer needle valve member. The outer needle valve member is a piece component that includes at least one external guide surface, an external value surface and an internal valve seat.

NOAA Education: Adventures in Strategic Planning, External Review, and Evaluation

NASA Astrophysics Data System (ADS)

Michalopoulos, C.

2010-12-01

Since late 2007, the National Oceanic and Atmospheric Administration has undertaken the development of a 20-year Education Strategic Plan, has undergone an external review by the National Research Council of the National Academies, and has drafted a guiding document on an agency-wide approach for monitoring and evaluation of its education activities and programs. This presentation will review all these processes with special emphasis on lessons learned and on the implications of each one on NOAA’s ability to improve and better coordinate its educational portfolio.

Relationship between relaxation by guided imagery and performance of working memory.

PubMed

Hudetz, J A; Hudetz, A G; Klayman, J

2000-02-01

This study tested the hypothesis that relaxation by guided imagery improves working-memory performance of healthy participants. 30 volunteers (both sexes, ages 17-56 years) were randomly assigned to one of three groups and administered the WAIS-III Letter-Number Sequencing Test before and after 10-min. treatment with guided imagery or popular music. The control group received no treatment. Groups' test scores were not different before treatment. The mean increased after relaxation by guided imagery but not after music or no treatment. This result supports the hypothesis that working-memory scores on the test are enhanced by guided imagery and implies that human information processing may be enhanced by prior relaxation.

Understanding the Stress Process of Chinese- and Korean-American Breast Cancer Survivors.

PubMed

Paek, Min-So; Lim, Jung-Won

2016-10-01

Guided by the stress process model (SPM), this study investigated the direct and indirect pathways of primary (negative self-image and life stress), secondary stressors (family communication strain) and family coping (external and internal) on mental health outcomes among Chinese- and Korean-American breast cancer survivors (BCS). A total of 156 Chinese- and Korean-American BCS were surveyed. Results showed primary and secondary stressors had a negative effect on better mental health outcomes. External coping was associated with better mental health. Family communication strain mediated the relationship between life stress and mental health outcomes. External coping mediated the relationship between family communication strain and mental health outcomes. Multi-group analysis revealed the stress process did not differ across ethnic groups. Findings suggest the SPM may be applicable to understand the stress process of Chinese- and Korean-American BCS and provide valuable insight into the role of family communication and external coping on mental health outcomes.

27nt-RNAs guide histone variant deposition via 'RNA-induced DNA replication interference' and thus transmit parental genome partitioning in Stylonychia.

PubMed

Postberg, Jan; Jönsson, Franziska; Weil, Patrick Philipp; Bulic, Aneta; Juranek, Stefan Andreas; Lipps, Hans-Joachim

2018-06-12

During sexual reproduction in the unicellular ciliate Stylonychia somatic macronuclei differentiate from germline micronuclei. Thereby, programmed sequence reduction takes place, leading to the elimination of > 95% of germline sequences, which priorly adopt heterochromatin structure via H3K27me3. Simultaneously, 27nt-ncRNAs become synthesized from parental transcripts and are bound by the Argonaute protein PIWI1. These 27nt-ncRNAs cover sequences destined to the developing macronucleus and are thought to protect them from degradation. We provide evidence and propose that RNA/DNA base-pairing guides PIWI1/27nt-RNA complexes to complementary macronucleus-destined DNA target sequences, hence transiently causing locally stalled replication during polytene chromosome formation. This spatiotemporal delay enables the selective deposition of temporarily available histone H3.4K27me3 nucleosomes at all other sequences being continuously replicated, thus dictating their prospective heterochromatin structure before becoming developmentally eliminated. Concomitantly, 27nt-RNA-covered sites remain protected. We introduce the concept of 'RNA-induced DNA replication interference' and explain how the parental functional genome partition could become transmitted to the progeny.

Argonaute-based programmable RNase as a tool for cleavage of highly-structured RNA.

PubMed

Dayeh, Daniel M; Cantara, William A; Kitzrow, Jonathan P; Musier-Forsyth, Karin; Nakanishi, Kotaro

2018-06-12

The recent identification and development of RNA-guided enzymes for programmable cleavage of target nucleic acids offers exciting possibilities for both therapeutic and biotechnological applications. However, critical challenges such as expensive guide RNAs and inability to predict the efficiency of target recognition, especially for highly-structured RNAs, remain to be addressed. Here, we introduce a programmable RNA restriction enzyme, based on a budding yeast Argonaute (AGO), programmed with cost-effective 23-nucleotide (nt) single-stranded DNAs as guides. DNA guides offer the advantage that diverse sequences can be easily designed and purchased, enabling high-throughput screening to identify optimal recognition sites in the target RNA. Using this DNA-induced slicing complex (DISC) programmed with 11 different guide DNAs designed to span the sequence, sites of cleavage were identified in the 352-nt human immunodeficiency virus type 1 5'-untranslated region. This assay, coupled with primer extension and capillary electrophoresis, allows detection and relative quantification of all DISC-cleavage sites simultaneously in a single reaction. Comparison between DISC cleavage and RNase H cleavage reveals that DISC not only cleaves solvent-exposed sites, but also sites that become more accessible upon DISC binding. This study demonstrates the advantages of the DISC system for programmable cleavage of highly-structured, functional RNAs.

Sequential addition of short DNA oligos in DNA-polymerase-based synthesis reactions

DOEpatents

Gardner, Shea N; Mariella, Jr., Raymond P; Christian, Allen T; Young, Jennifer A; Clague, David S

2013-06-25

A method of preselecting a multiplicity of DNA sequence segments that will comprise the DNA molecule of user-defined sequence, separating the DNA sequence segments temporally, and combining the multiplicity of DNA sequence segments with at least one polymerase enzyme wherein the multiplicity of DNA sequence segments join to produce the DNA molecule of user-defined sequence. Sequence segments may be of length n, where n is an odd integer. In one embodiment the length of desired hybridizing overlap is specified by the user and the sequences and the protocol for combining them are guided by computational (bioinformatics) predictions. In one embodiment sequence segments are combined from multiple reading frames to span the same region of a sequence, so that multiple desired hybridizations may occur with different overlap lengths.

On-the-fly detection of images with gastritis aspects in magnetically guided capsule endoscopy

NASA Astrophysics Data System (ADS)

Mewes, P. W.; Neumann, D.; Juloski, A. L.; Angelopoulou, E.; Hornegger, J.

2011-03-01

Capsule Endoscopy (CE) was introduced in 2000 and has since become an established diagnostic procedure for the small bowel, colon and esophagus. For the CE examination the patient swallows the capsule, which then travels through the gastrointestinal tract under the influence of the peristaltic movements. CE is not indicated for stomach examination, as the capsule movements can not be controlled from the outside and the entire surface of the stomach can not be reliably covered. Magnetically-guided capsule endoscopy (MGCE) was introduced in 2010. For the MGCE procedure the stomach is filled with water and the capsule is navigated from the outside using an external magnetic field. During the examination the operator can control the motion of the capsule in order to obtain a sufficient number of stomach-surface images with diagnostic value. The quality of the examination depends on the skill of the operator and his ability to detect aspects of interest in real time. We present a novel computer-assisted diagnostic-procedure (CADP) algorithm for indicating gastritis pathologies in the stomach during the examination. Our algorithm is based on pre-processing methods and feature vectors that are suitably chosen for the challenges of the MGCE imaging (suspended particles, bubbles, lighting). An image is classified using an ada-boost trained classifier. For the classifier training, a number of possible features were investigated. Statistical evaluation was conducted to identify relevant features with discriminative potential. The proposed algorithm was tested on 12 video sequences stemming from 6 volunteers. A mean detection rate of 91.17% was achieved during leave-one out cross-validation.

Prefrontal cholinergic mechanisms instigating shifts from monitoring for cues to cue-guided performance: Converging electrochemical and fMRI evidence from rats and humans

PubMed Central

Howe, William M.; Berry, Anne S.; Francois, Jennifer; Gilmour, Gary; Carp, Joshua M.; Tricklebank, Mark; Lustig, Cindy; Sarter, Martin

2013-01-01

We previously reported involvement of right prefrontal cholinergic activity in veridical signal detection. Here, we first recorded real-time acetylcholine release in prefrontal cortex during specific trial sequences in rats performing a task requiring signal detection as well as rejection of non-signal events. Cholinergic release events recorded with sub-second resolution (“transients”) were observed only during signal-hit trials, not during signal-miss trials or non-signal events. Moreover, cholinergic transients were not observed for consecutive hits; instead they were limited to signal-hit trials that were preceded by factual or perceived non-signal events (“incongruent hits”). This finding suggests that these transients mediate shifts from a state of perceptual attention, or monitoring for cues, to cue-evoked activation of response rules and the generation of a cue-directed response. Next, to determine the translational significance of the cognitive operations supporting incongruent hits we employed a version of the task previously validated for use in research in humans and BOLD-fMRI. Incongruent hits activated a region in the right rostral prefrontal cortex (BA 10). Furthermore, greater prefrontal activation was correlated with faster response times for incongruent hits. Finally, we measured tissue oxygen in rats, as a proxy for BOLD, and found prefrontal increases in oxygen levels solely during incongruent hits. These cross-species studies link a cholinergic response to a prefrontal BOLD activation and indicate that these interrelated mechanisms mediate the integration of external cues with internal representations to initiate and guide behavior. PMID:23678117

Introduction to Engineering. Course I: Challenges of Engineering. Course II: Engineering Projects.

ERIC Educational Resources Information Center

Barrier, Lynn P.

This guide, which is designed to be used in a two-course sequence, is intended to prepare college-bound high school juniors and seniors for engineering and related courses at the college level. The guide was developed as part of an experimental competency-based curriculum that integrates the high-tech applications of mathematics and science…

The Heart of Matter: A Nuclear Chemistry Module. Teacher's Guide.

ERIC Educational Resources Information Center

Viola, Vic; Hearle, Robert

This teacher's guide is designed to provide science teachers with the necessary guidance and suggestions for teaching nuclear chemistry. In this book, the fundamental concepts of nuclear science and the applications of nuclear energy are discussed. The material in this book can be integrated with the other modules in a sequence that helps students…

Conservation for Children [Levels 1-6 and an All-Levels Supplement].

ERIC Educational Resources Information Center

Cupertino Union School District, CA.

Developed to promote conservation awareness in elementary students, each of the six grade-level-sequenced activity guides provides: (1) a list of conservation concepts; (2) a criterion-referenced test; (3) a class record sheet; (4) a content guide; and (5) 90 student worksheets (40 for language arts, 20 for mathematics, 20 for social studies and…

Elementary Art Constructions: A Supplement to the Elementary Art Guide 1968.

ERIC Educational Resources Information Center

Lundman, Donald; And Others

GRADES OR AGES: K-6. SUBJECT MATTER: Elementary Art--Constructions. ORGANIZATION AND PHYSICAL APPEARANCE: After a brief introduction and a scope and sequence chart, the guide is divided into seven sections, one for each grade covered, and these sections contain details for between three and nine projects, including the making of cheese boards,…

Crawling and/or Squatting: A Saleable Work Skill. Occupation Simulation Packet. Grades K-2nd.

ERIC Educational Resources Information Center

Montgomery, Margery

This teacher's guide for grades K-2 contains simulated work experiences for students using the isolated skill concept, crawling and/or squatting. Teacher instructions include objectives, evaluation, and sequence of activities. The guide contains pre-tests and post-tests with instructions and answer keys. Three pre-skill activities are suggested,…

Health Education Resource Guide, Grades 1-3.

ERIC Educational Resources Information Center

Federal Way School District 210, WA.

As part of a health education program for K-12, these curriculum guides for grades one, two and three provide: (1) a short overview of health education; (2) a scope and sequence chart which lists specific topics to teach on mental health, physical health, community health, and safety that are appropriate at different grade levels; (3) a list of…

Grain, Feed, Seed, and Farm Supply Technology. A Suggested 2-Year Post High School Curriculum.

ERIC Educational Resources Information Center

Office of Education (DHEW), Washington, DC.

The increasing need for skilled agricultural technicians for the grain, feed, seed, and farm supply industry resulted in preparation of this suggested curriculum guide to aid in planning, developing, and evaluating post-high school programs. The guide includes: (1) suggested course outlines with examples of texts and references, (2) sequence of…

Elementary Science Curriculum, Grade 5.

ERIC Educational Resources Information Center

Stoneham Public Schools, MA.

This is one of a set of curriculum guides for the Stoneham Elementary School Science Program (see SE 012 153 - SE 012 158). Each guide contains a chart illustrating the scope and sequence of the physical, life, and earth sciences introduced at each grade level. For each of the topics introduced at this grade level an overview of the topic, a list…

Classroom Archaeology: An Archaeology Activity Guide for Teachers. Third Edition.

ERIC Educational Resources Information Center

Hawkins, Nancy W.

This guide describes archaeology activities appropriate for middle school students, but some activities can be used in intermediate and primary grades or high school and college classes. The activities range in length from less than one hour to 15 hours. A sequence of activities may be used together as a unit on archaeology, or individual…

Access: A Guide to Finding Community Services. Project STEPS (Sequenced Transition to Education in the Public Schools).

ERIC Educational Resources Information Center

Byrd, Rita, Comp.; And Others

This guide is intended to help Kentucky families of children with disabilities or other special needs to find services in their communities. Introductory information offers guidance in selecting services, applying for services, obtaining services, and organizing to obtain unavailable services. A question-and-answer format is used, with space…

Elementary Science Curriculum, Grade 6.

ERIC Educational Resources Information Center

Stoneham Public Schools, MA.

This is one of a set of curriculum guides for the Stoneham Elementary School Science Program (see SE 012 153 - SE 012 158). Each guide contains a chart illustrating the scope and sequence of the physical, life, and earth sciences introduced at each grade level. For each of the topics introduced at this grade level an overview of the topic, a list…

Health Education Resource Guide, Junior High.

ERIC Educational Resources Information Center

Federal Way School District 210, WA.

As part of a health education program for K-12, this curriculum guide for grade eight provides: (1) a short overview of health education; (2) a scope and sequence chart which lists specific topics to teach on mental health, physical health, community health, and safety that are appropriate at different grade levels; (3) a list of objectives; and…

Oral Persuasion: A Saleable Work Skill. Occupation Simulation Packet. Grades 5th-6th.

ERIC Educational Resources Information Center

Lee, Dennis W.

This teacher's guide contains simulated work experiences for 5th and 6th grade students using the isolated skill concept - oral persuasion. Teacher instructions include objectives, evaluation, and sequence of activities. The guide contains pre-tests and post-tests with instructions and answer keys. Two pre-skill activities are suggested, such as…

Form and Function: An Organic Chemistry Module. Teacher's Guide.

ERIC Educational Resources Information Center

Jarvis, Bruce; Mazzocchi, Paul; Hearle, Robert

This teacher's guide is designed to provide science teachers with the necessary guidance and suggestions for teaching organic chemistry. In this book, the diverse field of organic chemistry modules is introduced. The material in this book can be integrated with the other modules in a sequence that helps students to see that chemistry is a unified…

An arbitrary grid CFD algorithm for configuration aerodynamics analysis. Volume 2: FEMNAS user guide

NASA Technical Reports Server (NTRS)

Manhardt, Paul D.; Orzechowski, J. A.; Baker, A. J.

1992-01-01

This report documents the user input and output data requirements for the FEMNAS finite element Navier-Stokes code for real-gas simulations of external aerodynamics flowfields. This code was developed for the configuration aerodynamics branch of NASA ARC, under SBIR Phase 2 contract NAS2-124568 by Computational Mechanics Corporation (COMCO). This report is in two volumes. Volume 1 contains the theory for the derived finite element algorithm and describes the test cases used to validate the computer program described in the Volume 2 user guide.

Vertical decomposition with Genetic Algorithm for Multiple Sequence Alignment

PubMed Central

2011-01-01

Background Many Bioinformatics studies begin with a multiple sequence alignment as the foundation for their research. This is because multiple sequence alignment can be a useful technique for studying molecular evolution and analyzing sequence structure relationships. Results In this paper, we have proposed a Vertical Decomposition with Genetic Algorithm (VDGA) for Multiple Sequence Alignment (MSA). In VDGA, we divide the sequences vertically into two or more subsequences, and then solve them individually using a guide tree approach. Finally, we combine all the subsequences to generate a new multiple sequence alignment. This technique is applied on the solutions of the initial generation and of each child generation within VDGA. We have used two mechanisms to generate an initial population in this research: the first mechanism is to generate guide trees with randomly selected sequences and the second is shuffling the sequences inside such trees. Two different genetic operators have been implemented with VDGA. To test the performance of our algorithm, we have compared it with existing well-known methods, namely PRRP, CLUSTALX, DIALIGN, HMMT, SB_PIMA, ML_PIMA, MULTALIGN, and PILEUP8, and also other methods, based on Genetic Algorithms (GA), such as SAGA, MSA-GA and RBT-GA, by solving a number of benchmark datasets from BAliBase 2.0. Conclusions The experimental results showed that the VDGA with three vertical divisions was the most successful variant for most of the test cases in comparison to other divisions considered with VDGA. The experimental results also confirmed that VDGA outperformed the other methods considered in this research. PMID:21867510

A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics

PubMed Central

Tang, Haixu; Li, Sujun; Ye, Yuzhen

2016-01-01

Metaproteomic studies adopt the common bottom-up proteomics approach to investigate the protein composition and the dynamics of protein expression in microbial communities. When matched metagenomic and/or metatranscriptomic data of the microbial communities are available, metaproteomic data analyses often employ a metagenome-guided approach, in which complete or fragmental protein-coding genes are first directly predicted from metagenomic (and/or metatranscriptomic) sequences or from their assemblies, and the resulting protein sequences are then used as the reference database for peptide/protein identification from MS/MS spectra. This approach is often limited because protein coding genes predicted from metagenomes are incomplete and fragmental. In this paper, we present a graph-centric approach to improving metagenome-guided peptide and protein identification in metaproteomics. Our method exploits the de Bruijn graph structure reported by metagenome assembly algorithms to generate a comprehensive database of protein sequences encoded in the community. We tested our method using several public metaproteomic datasets with matched metagenomic and metatranscriptomic sequencing data acquired from complex microbial communities in a biological wastewater treatment plant. The results showed that many more peptides and proteins can be identified when assembly graphs were utilized, improving the characterization of the proteins expressed in the microbial communities. The additional proteins we identified contribute to the characterization of important pathways such as those involved in degradation of chemical hazards. Our tools are released as open-source software on github at https://github.com/COL-IU/Graph2Pro. PMID:27918579

Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale

PubMed Central

Schmidt, Thomas S. B.; Matias Rodrigues, João F.; von Mering, Christian

2014-01-01

Operational Taxonomic Units (OTUs), usually defined as clusters of similar 16S/18S rRNA sequences, are the most widely used basic diversity units in large-scale characterizations of microbial communities. However, it remains unclear how well the various proposed OTU clustering algorithms approximate ‘true’ microbial taxa. Here, we explore the ecological consistency of OTUs – based on the assumption that, like true microbial taxa, they should show measurable habitat preferences (niche conservatism). In a global and comprehensive survey of available microbial sequence data, we systematically parse sequence annotations to obtain broad ecological descriptions of sampling sites. Based on these, we observe that sequence-based microbial OTUs generally show high levels of ecological consistency. However, different OTU clustering methods result in marked differences in the strength of this signal. Assuming that ecological consistency can serve as an objective external benchmark for cluster quality, we conclude that hierarchical complete linkage clustering, which provided the most ecologically consistent partitions, should be the default choice for OTU clustering. To our knowledge, this is the first approach to assess cluster quality using an external, biologically meaningful parameter as a benchmark, on a global scale. PMID:24763141

Excess spontaneous emission in non-Hermitian optical systems. I. Laser amplifiers

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

Siegman, A.E.

1989-02-01

Petermann first predicted in 1979 the existence of an excess-spontaneous-emission factor in gain-guided semiconductor lasers. We show that an excess spontaneous emission of this type, and also a correlation between the spontaneous emission into different cavity modes, will in fact be present in all open-sided laser resonators or optical lens guides. These properties arise from the non-self-adjoint or non-power-orthogonal nature of the optical resonator modes. The spontaneous-emission rate is only slightly enhanced in stable-resonator or index-guided structures, but can become very much larger than normal in gain-guided or geometrically unstable structures. Optical resonators or lens guides that have an excessmore » noise emission necessarily also exhibit an ''excess initial-mode excitation factor'' for externally injected signals. As a result, the excess spontaneous emission can be balanced out and the usual quantum-noise limit recovered in laser amplifiers and in injection-seeded laser oscillators, but not in free-running laser oscillators.« less

Transition to Science Teacher Educator: Tensions Experienced While Learning to Teach Lesson Sequencing

ERIC Educational Resources Information Center

Wiebke, Heidi; Park Rogers, Meredith

2014-01-01

This self-study investigated the tensions that I (Heidi) encountered when teaching elementary preservice teachers how to develop a coherent sequence of five science lessons. Four lesson planning components guided me in developing a series of lessons to support the preservice teachers with this exercise. Employing self-study methodology, data…

Filter Presses. Sludge Treatment and Disposal Course #166. Instructor's Guide [and] Student Workbook.

ERIC Educational Resources Information Center

Alloway, Rawle A.

This lesson is an introduction to the operation of filter presses. Two basic types of presses, their components, the sequence of operation, operational controls, sampling, and testing are discussed. The instructor's manual contains a description of the lesson, estimated presentation time, instructional materials list, suggested sequence of…

Laser-guided energetic discharges over large air gaps by electric-field enhanced plasma filaments

NASA Astrophysics Data System (ADS)

Théberge, Francis; Daigle, Jean-François; Kieffer, Jean-Claude; Vidal, François; Châteauneuf, Marc

2017-01-01

Recent works on plasma channels produced during the propagation of ultrashort and intense laser pulses in air demonstrated the guiding of electric discharges along the laser path. However, the short plasma lifetime limits the length of the laser-guided discharge. In this paper, the conductivity and lifetime of long plasma channels produced by ultrashort laser pulses is enhanced efficiently over many orders of magnitude by the electric field of a hybrid AC-DC high-voltage source. The AC electric pulse from a Tesla coil allowed to stimulate and maintain the highly conductive channel during few milliseconds in order to guide a subsequent 500 times more energetic discharge from a 30-kV DC source. This DC discharge was laser-guided over an air gap length of two metres, which is more than two orders of magnitude longer than the expected natural discharge length. Long plasma channel induced by laser pulses and stimulated by an external high-voltage source opens the way for wireless and efficient transportation of energetic current pulses over long air gaps and potentially for guiding lightning.

Dental Shade Guide Variability for Hues B, C, and D Using Cross-Polarized Photography.

PubMed

Sampaio, Camila S; Gurrea, Jon; Gurrea, Marta; Bruguera, August; Atria, Pablo J; Janal, Malvin; Bonfante, Estevam A; Coelho, Paulo G; Hirata, Ronaldo

2018-04-20

This study evaluated the color variability of hues B, C, and D between the VITA Classical shade guide (Vita Zahnfabrik) and four other VITA-coded ceramic shade guides using a digital camera (Canon EOS 60D) and computer software (Adobe Photoshop CC). A cross-polarizing filter was used to standardize external light sources influencing color match. A total of 275 pictures were taken, 5 per shade tab, for 11 shades (B1, B2, B3, B4, C1, C2, C3, C4, D2, D3, and D4), from the following shade guides: VITA Classical (control); IPS e.max Ceram (Ivoclar Vivadent); IPS d.SIGN (Ivoclar Vivadent); Initial ZI (GC); and Creation CC (Creation Willi Geller). Pictures were evaluated using Adobe Photoshop CC for standardization of hue, chroma, and value between shade tabs. The VITA-coded shade guides evaluated here showed an overall unmatched shade in all their tabs when compared to the control, suggesting that shade selection should be made with the corresponding manufacturer guide of the ceramic intended for the final restoration.

Laser-guided energetic discharges over large air gaps by electric-field enhanced plasma filaments

PubMed Central

Théberge, Francis; Daigle, Jean-François; Kieffer, Jean-Claude; Vidal, François; Châteauneuf , Marc

2017-01-01

Recent works on plasma channels produced during the propagation of ultrashort and intense laser pulses in air demonstrated the guiding of electric discharges along the laser path. However, the short plasma lifetime limits the length of the laser-guided discharge. In this paper, the conductivity and lifetime of long plasma channels produced by ultrashort laser pulses is enhanced efficiently over many orders of magnitude by the electric field of a hybrid AC-DC high-voltage source. The AC electric pulse from a Tesla coil allowed to stimulate and maintain the highly conductive channel during few milliseconds in order to guide a subsequent 500 times more energetic discharge from a 30-kV DC source. This DC discharge was laser-guided over an air gap length of two metres, which is more than two orders of magnitude longer than the expected natural discharge length. Long plasma channel induced by laser pulses and stimulated by an external high-voltage source opens the way for wireless and efficient transportation of energetic current pulses over long air gaps and potentially for guiding lightning. PMID:28053312

TU-AB-BRA-07: Distortion-Free 3D Diffusion MRI On An MRI-Guided Radiotherapy System for Longitudinal Tumor Response Assessment

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

Gao, Y; Yang, Y; Rangwala, N

Purpose: To develop a reliable, 3D distortion-free diffusion MRI technique for longitudinal tumor response assessment and MRI-guided adaptive radiotherapy(RT). Methods: A diffusion prepared 3D turbo spin echo readout (DP-TSE) sequence was developed and compared with the conventional diffusion-weighted single-shot echo-planar-imaging (DW-ssEPI) sequence in a commercially available diffusion phantom, and one head-and-neck and one brain cancer patient on an MRI-guided RT system (ViewRay). In phantom study, the geometric fidelity was quantified as the ratio between the left-right (RL) and anterior-posterior (AP) dimension. Ten slices were measured on DP-TSE, DW-ssEPI and standard TSE images where the later was used as the geometricmore » reference. ADC accuracy was verified at both 0°C (reference ADC available) and room temperature with a range of diffusivity between 0.35 and 2.0*10{sup −3}mm{sup 2}/s. The ADC reproducibility was assessed based on 8 room-temperature measurements on 6 different days. In the pilot single-slice in-vivo study, CT images were used as the geometric reference, and ADC maps from both diffusion sequences were compared. Results: Distortion and susceptive-related artifact were severe in DW-ssEPI, with significantly lower RL/AP ratio (0.9579±0.0163) than DP-TSE (0.9990±0.0031) and TSE (0.9995±0.0031). ADCs from the two diffusion sequences both matched well with the vendor-provided values at 0°C; however DW-ssEPI fails to provide accurate ADC for high diffusivity vials at room temperature due to high noise level (10 times higher than DP-TSE). The DP-TSE sequence had excellent ADC reproducibility with <4% ADC variation among 8 separate measurements. In patient study, DP-TSE exhibited substantially improved geometric reliability. ROI analysis in ADC maps generated from DP-TSE and DW-ssEPI showed <5% difference where high b-value images were excluded from the latter approach due to excessive noise level. Conclusion: A diffusion MRI sequence with excellent geometric fidelity, accurate and highly reproducible ADC measurements was proposed for longitudinal tumor response assessment using an MRI-guided RT system. Yu Gao acknowledges research support from ViewRay.« less

Functional DNA quantification guides accurate next-generation sequencing mutation detection in formalin-fixed, paraffin-embedded tumor biopsies

PubMed Central

2013-01-01

The formalin-fixed, paraffin-embedded (FFPE) biopsy is a challenging sample for molecular assays such as targeted next-generation sequencing (NGS). We compared three methods for FFPE DNA quantification, including a novel PCR assay (‘QFI-PCR’) that measures the absolute copy number of amplifiable DNA, across 165 residual clinical specimens. The results reveal the limitations of commonly used approaches, and demonstrate the value of an integrated workflow using QFI-PCR to improve the accuracy of NGS mutation detection and guide changes in input that can rescue low quality FFPE DNA. These findings address a growing need for improved quality measures in NGS-based patient testing. PMID:24001039

Endothelial cell motility, coordination and pattern formation during vasculogenesis.

PubMed

Czirok, Andras

2013-01-01

How vascular networks assemble is a fundamental problem of developmental biology that also has medical importance. To explain the organizational principles behind vascular patterning, we must understand how can tissue level structures be controlled through cell behavior patterns like motility and adhesion that, in turn, are determined by biochemical signal transduction processes? We discuss the various ideas that have been proposed as mechanisms for vascular network assembly: cell motility guided by extracellular matrix alignment (contact guidance), chemotaxis guided by paracrine and autocrine morphogens, and multicellular sprouting guided by cell-cell contacts. All of these processes yield emergent patterns, thus endothelial cells can form an interconnected structure autonomously, without guidance from an external pre-pattern. © 2013 Wiley Periodicals, Inc.

Multi-modal and targeted imaging improves automated mid-brain segmentation

NASA Astrophysics Data System (ADS)

Plassard, Andrew J.; D'Haese, Pierre F.; Pallavaram, Srivatsan; Newton, Allen T.; Claassen, Daniel O.; Dawant, Benoit M.; Landman, Bennett A.

2017-02-01

The basal ganglia and limbic system, particularly the thalamus, putamen, internal and external globus pallidus, substantia nigra, and sub-thalamic nucleus, comprise a clinically relevant signal network for Parkinson's disease. In order to manually trace these structures, a combination of high-resolution and specialized sequences at 7T are used, but it is not feasible to scan clinical patients in those scanners. Targeted imaging sequences at 3T such as F-GATIR, and other optimized inversion recovery sequences, have been presented which enhance contrast in a select group of these structures. In this work, we show that a series of atlases generated at 7T can be used to accurately segment these structures at 3T using a combination of standard and optimized imaging sequences, though no one approach provided the best result across all structures. In the thalamus and putamen, a median Dice coefficient over 0.88 and a mean surface distance less than 1.0mm was achieved using a combination of T1 and an optimized inversion recovery imaging sequences. In the internal and external globus pallidus a Dice over 0.75 and a mean surface distance less than 1.2mm was achieved using a combination of T1 and FGATIR imaging sequences. In the substantia nigra and sub-thalamic nucleus a Dice coefficient of over 0.6 and a mean surface distance of less than 1.0mm was achieved using the optimized inversion recovery imaging sequence. On average, using T1 and optimized inversion recovery together produced significantly improved segmentation results than any individual modality (p<0.05 wilcox sign-rank test).

How Messenger RNA and Nascent Chain Sequences Regulate Translation Elongation.

PubMed

Choi, Junhong; Grosely, Rosslyn; Prabhakar, Arjun; Lapointe, Christopher P; Wang, Jinfan; Puglisi, Joseph D

2018-06-20

Translation elongation is a highly coordinated, multistep, multifactor process that ensures accurate and efficient addition of amino acids to a growing nascent-peptide chain encoded in the sequence of translated messenger RNA (mRNA). Although translation elongation is heavily regulated by external factors, there is clear evidence that mRNA and nascent-peptide sequences control elongation dynamics, determining both the sequence and structure of synthesized proteins. Advances in methods have driven experiments that revealed the basic mechanisms of elongation as well as the mechanisms of regulation by mRNA and nascent-peptide sequences. In this review, we highlight how mRNA and nascent-peptide elements manipulate the translation machinery to alter the dynamics and pathway of elongation.

Automatic Substitute Computed Tomography Generation and Contouring for Magnetic Resonance Imaging (MRI)-Alone External Beam Radiation Therapy From Standard MRI Sequences

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

Dowling, Jason A., E-mail: jason.dowling@csiro.au; University of Newcastle, Callaghan, New South Wales; Sun, Jidi

Purpose: To validate automatic substitute computed tomography CT (sCT) scans generated from standard T2-weighted (T2w) magnetic resonance (MR) pelvic scans for MR-Sim prostate treatment planning. Patients and Methods: A Siemens Skyra 3T MR imaging (MRI) scanner with laser bridge, flat couch, and pelvic coil mounts was used to scan 39 patients scheduled for external beam radiation therapy for localized prostate cancer. For sCT generation a whole-pelvis MRI scan (1.6 mm 3-dimensional isotropic T2w SPACE [Sampling Perfection with Application optimized Contrasts using different flip angle Evolution] sequence) was acquired. Three additional small field of view scans were acquired: T2w, T2*w, and T1wmore » flip angle 80° for gold fiducials. Patients received a routine planning CT scan. Manual contouring of the prostate, rectum, bladder, and bones was performed independently on the CT and MR scans. Three experienced observers contoured each organ on MRI, allowing interobserver quantification. To generate a training database, each patient CT scan was coregistered to their whole-pelvis T2w using symmetric rigid registration and structure-guided deformable registration. A new multi-atlas local weighted voting method was used to generate automatic contours and sCT results. Results: The mean error in Hounsfield units between the sCT and corresponding patient CT (within the body contour) was 0.6 ± 14.7 (mean ± 1 SD), with a mean absolute error of 40.5 ± 8.2 Hounsfield units. Automatic contouring results were very close to the expert interobserver level (Dice similarity coefficient): prostate 0.80 ± 0.08, bladder 0.86 ± 0.12, rectum 0.84 ± 0.06, bones 0.91 ± 0.03, and body 1.00 ± 0.003. The change in monitor units between the sCT-based plans relative to the gold standard CT plan for the same dose prescription was found to be 0.3% ± 0.8%. The 3-dimensional γ pass rate was 1.00 ± 0.00 (2 mm/2%). Conclusions: The MR-Sim setup and automatic sCT generation methods using standard MR sequences generates realistic contours and electron densities for prostate cancer radiation therapy dose planning and digitally reconstructed radiograph generation.« less

MR-guided prostate interventions.

PubMed

Tempany, Clare; Straus, Sarah; Hata, Nobuhiko; Haker, Steven

2008-02-01

In this article the current issues of diagnosis and detection of prostate cancer are reviewed. The limitations for current techniques are highlighted and some possible solutions with MR imaging and MR-guided biopsy approaches are reviewed. There are several different biopsy approaches under investigation. These include transperineal open magnet approaches to closed-bore 1.5T transrectal biopsies. The imaging, image processing, and tracking methods are also discussed. In the arena of therapy, MR guidance has been used in conjunction with radiation methods, either brachytherapy or external delivery. The principles of the radiation treatment, the toxicities, and use of images are outlined. The future role of imaging and image-guided interventions lie with providing a noninvasive surrogate for cancer surveillance or monitoring treatment response. The shift to minimally invasive focal therapies has already begun and will be very exciting when MR-guided focused ultrasound surgery reaches its full potential. (Copyright) 2008 Wiley-Liss, Inc.

MR-Guided Prostate Interventions

PubMed Central

Tempany, Clare; Straus, Sarah; Hata, Nobuhiko; Haker, Steven

2009-01-01

In this article the current issues of diagnosis and detection of prostate cancer are reviewed. The limitations for current techniques are highlighted and some possible solutions with MR imaging and MR-guided biopsy approaches are reviewed. There are several different biopsy approaches under investigation. These include transperineal open magnet approaches to closed-bore 1.5T transrectal biopsies. The imaging, image processing, and tracking methods are also discussed. In the arena of therapy, MR guidance has been used in conjunction with radiation methods, either brachytherapy or external delivery. The principles of the radiation treatment, the toxicities, and use of images are outlined. The future role of imaging and image-guided interventions lie with providing a noninvasive surrogate for cancer surveillance or monitoring treatment response. The shift to minimally invasive focal therapies has already begun and will be very exciting when MR-guided focused ultrasound surgery reaches its full potential. PMID:18219689

Maintaining the Median in Early Childhood Educational Methodology

ERIC Educational Resources Information Center

Hewes, Dorothy W.

2005-01-01

History shows that educational systems and educational theorists have consciously or unconsciously structured the education of young children toward one end or the other of the continuum between "internals" and "externals". Systems in which teacher-guided learning was based on efforts to satisfy individual needs, systems that…

The University as Microcosm

ERIC Educational Resources Information Center

Kaldis, Byron

2009-01-01

This paper puts forward the model of "microcosm-macrocosm" isomorphism encapsulated in certain philosophical views on the form of university education. The human being as a "microcosm" should reflect internally the external "macrocosm". Higher Education is a socially instituted attempt to guide human beings into forming themselves as microcosms of…

Management Training in Retailing.

ERIC Educational Resources Information Center

Veness, C. Rosina

Intended for prospective members of the new Distributive Industrial Training Board in Great Britain, this training guide concentrates on managerial functions in retailing; the selection of trainees; the planning of in-company and external training programs; scheduling and continuity of training; roles of training personnel; and the use of various…

Performance Indicators (for Kindergartens). (First Edition).

ERIC Educational Resources Information Center

Hong Kong Education Dept.

As part of the 1999 comprehensive review of the education system in Hong Kong, the Education Department introduced a quality assurance framework in local kindergartens. The framework comprises two components: self-evaluation and external monitoring. This guide presents performance indicators for use as evaluation criteria with reference to the…

An Administrator's Guide to Installing a Telephone System.

ERIC Educational Resources Information Center

Forbes, Phyllis Rossiter

1986-01-01

Guidelines for administrators concerning installation of a new campus telephone system address these issues: where to start; location and emergency power; the project team; paperwork; communication among those involved in installation; working with the local operating company; existing wiring; the external cable plant; special needs; and training…

Perceptions of STEM-Based Outreach Learning Activities in Secondary Education

ERIC Educational Resources Information Center

Vennix, J.; den Brok, P.; Taconis, R.

2017-01-01

We investigated and compared the learning environment perceptions of students, teachers and guides who participated in Science, Technology, Engineering and Mathematics (STEM)-based outreach activities in secondary education. In outreach activities, schools and teachers work together with companies and other external institutions in learning…

Assessment of progressively delayed prompts on guided skill learning in rats.

PubMed

Reid, Alliston K; Futch, Sara E; Ball, Katherine M; Knight, Aubrey G; Tucker, Martha

2017-03-01

We examined the controlling factors that allow a prompted skill to become autonomous in a discrete-trials implementation of Touchette's (1971) progressively delayed prompting procedure, but our subjects were rats rather than children with disabilities. Our prompted skill was a left-right lever-press sequence guided by two panel lights. We manipulated (a) the effectiveness of the guiding lights prompt and (b) the presence or absence of a progressively delayed prompt in four groups of rats. The less effective prompt yielded greater autonomy than the more effective prompt. The ability of the progressively delayed prompt procedure to produce behavioral autonomy depended upon characteristics of the obtained delay (trial duration) rather than on the pending prompt. Sequence accuracy was reliably higher in unprompted trials than in prompted trials, and this difference was maintained in the 2 groups that received no prompts but yielded equivalent trial durations. Overall sequence accuracy decreased systematically as trial duration increased. Shorter trials and their greater accuracy were correlated with higher overall reinforcement rates for faster responding. Waiting for delayed prompts (even if no actual prompt was provided) was associated with lower overall reinforcement rate by decreasing accuracy and by lengthening trials. These findings extend results from previous studies regarding the controlling factors in delayed prompting procedures applied to children with disabilities.

Energy--Structure--Life. A Learning System for Understanding Science, Book Two.

ERIC Educational Resources Information Center

Bixby, Louis W.; And Others

This learning guide contains materials for the second year of Energy/Structure/ Life, a two year high school program in integrated science. The guide is programed to permit the student to proceed on his own at a self-determined pace. The two year course is a sequence of physics, chemistry, and biology with the chemical (continued from the first…

The Incredible Egg. 4-H Classroom Curriculum Guide for Grade Levels 4-5.

ERIC Educational Resources Information Center

Ohio State Univ., Columbus. Cooperative Extension Service.

This curriculum guide integrates the concepts of chick embryology into mathematics, science, and language arts lesson plans for Grades 4 and 5. The four lessons comprising the unit can be utilized in sequence or as independent lessons within the classroom curriculum. Lesson 1 enables students to identify the parts of an egg. Lesson 2 examines the…

Image Display And Manipulation System (IDAMS), user's guide

NASA Technical Reports Server (NTRS)

Cecil, R. W.

1972-01-01

A combination operator's guide and user's handbook for the Image Display and Manipulation System (IDAMS) is reported. Information is presented to define how to operate the computer equipment, how to structure a run deck, and how to select parameters necessary for executing a sequence of IDAMS task routines. If more detailed information is needed on any IDAMS program, see the IDAMS program documentation.

GROUNDWARS 4.2 Reference Guide

DTIC Science & Technology

1991-12-01

land duel , homogeneous forces, TANKWARS, target acquisition, combat survivability 19. ABSTRACT (Continue on reverse if necessary and identify by block...number) GROUNDWARS is a stochastic, two-sided, event-sequenced weapon systems effectiveness model which provides the results of a land duel between two...GROUNDWARS 4.2 REFERENCE GUIDE I. INTRODUCTION Groundwars is a weapon systems effectiveness model which provides the results of a land duel between

Madison Public Schools. La Follette Careers Program. Tenth Grade Social Studies Guide.

ERIC Educational Resources Information Center

Morrissey, Jim; Waity, Charles

A social studies course for a tenth grade career program is outlined in this curriculum and teaching guide. A calendar plots the time sequence for the nine units which cover prehistory to the present. The format of each unit is in three sections. The interrelated concepts, behavior goals, and teaching methods and learning activities are presented,…

From Cooks to Carpenters: Measuring - A Saleable Work Skill. Occupation Simulation Packet. Grades 5th-6th.

ERIC Educational Resources Information Center

Kennedy, Helena

This teacher's guide contains simulated work experiences for 5th and 6th grade students using the isolated skill concept - measuring. Teacher instructions include objectives, evaluation, and sequence of activities. The guide contains pre-tests and post-tests with instructions and answer keys. Three pre-skill activities are suggested, such as…

Genreflecting: A Guide to Reading Interests in Genre Fiction. Fourth Edition.

ERIC Educational Resources Information Center

Herald, Diana Tixier

Neither a bibliography nor a history of genres through historical sequences of listings by author, this book is a guide for those who help readers identify genre authors and titles of desired types in both libraries and bookstores. A secondary purpose of the book is as a text for library school students, aimed at familiarizing them with the common…

Origin of Polar Order in Dense Suspensions of Phototactic Micro-Swimmers

PubMed Central

Furlan, Silvano; Comparini, Diego; Ciszak, Marzena; Beccai, Lucia; Mancuso, Stefano; Mazzolai, Barbara

2012-01-01

A main question for the study of collective motion in living organisms is the origin of orientational polar order, i.e., how organisms align and what are the benefits of such collective behaviour. In the case of micro-organisms swimming at a low Reynolds number, steric repulsion and long-range hydrodynamic interactions are not sufficient to explain a homogeneous polar order state in which the direction of motion is aligned. An external symmetry-breaking guiding field such as a mechanism of taxis appears necessary to understand this phonemonon. We have investigated the onset of polar order in the velocity field induced by phototaxis in a suspension of a motile micro-organism, the algae Chlamydomonas reinhardtii, for density values above the limit provided by the hydrodynamic approximation of a force dipole model. We show that polar order originates from a combination of both the external guiding field intensity and the population density. In particular, we show evidence for a linear dependence of a phototactic guiding field on cell density to determine the polar order for dense suspensions and demonstrate the existence of a density threshold for the origin of polar order. This threshold represents the density value below which cells undergoing phototaxis are not able to maintain a homogeneous polar order state and marks the transition to ordered collective motion. Such a transition is driven by a noise dominated phototactic reorientation where the noise is modelled as a normal distribution with a variance that is inversely proportional to the guiding field strength. Finally, we discuss the role of density in dense suspensions of phototactic micro-swimmers. PMID:22723904

Intermediate-term results of image-guided brachytherapy and high-technology external beam radiotherapy in cervical cancer: Chiang Mai University experience.

PubMed

Tharavichitkul, Ekkasit; Chakrabandhu, Somvilai; Wanwilairat, Somsak; Tippanya, Damrongsak; Nobnop, Wannapha; Pukanhaphan, Nantaka; Galalae, Razvan M; Chitapanarux, Imjai

2013-07-01

To evaluate the outcomes of image-guided brachytherapy combined with 3D conformal or intensity modulated external beam radiotherapy (3D CRT/IMRT) in cervical cancer at Chiang Mai University. From 2008 to 2011, forty-seven patients with locally advanced cervical cancer were enrolled in this study. All patients received high-technology (3D CRT/IMRT) whole pelvic radiotherapy with a total dose of 45-46 Gy plus image-guided High-Dose-Rate intracavitary brachytherapy 6.5-7 Gy × 4 fractions to a High-Risk Clinical Target Volume (HR-CTV) according to GEC-ESTRO recommendations. The dose parameters of the HR-CTV for bladder, rectum and sigmoid colon were recorded, as well as toxicity profiles. In addition, the endpoints for local control, disease-free, metastasis-free survival and overall survival were calculated. At the median follow-up time of 26 months, the local control, disease-free survival, and overall survival rates were 97.9%, 85.1%, and 93.6%, respectively. The mean dose of HR-CTV, bladder, rectum and sigmoid were 93.1, 88.2, 69.6, and 72 Gy, respectively. In terms of late toxicity, the incidence of grade 3-4 bladder and rectum morbidity was 2.1% and 2.1%, respectively. A combination of image-guided brachytherapy and IMRT/3D CRT showed very promising results of local control, disease-free survival, metastasis-free survival and overall survival rates. It also caused a low incidence of grade 3-4 toxicity in treated study patients. Copyright © 2013 Elsevier Inc. All rights reserved.

A user's guide to quantitative and comparative analysis of metagenomic datasets.

PubMed

Luo, Chengwei; Rodriguez-R, Luis M; Konstantinidis, Konstantinos T

2013-01-01

Metagenomics has revolutionized microbiological studies during the past decade and provided new insights into the diversity, dynamics, and metabolic potential of natural microbial communities. However, metagenomics still represents a field in development, and standardized tools and approaches to handle and compare metagenomes have not been established yet. An important reason accounting for the latter is the continuous changes in the type of sequencing data available, for example, long versus short sequencing reads. Here, we provide a guide to bioinformatic pipelines developed to accomplish the following tasks, focusing primarily on those developed by our team: (i) assemble a metagenomic dataset; (ii) determine the level of sequence coverage obtained and the amount of sequencing required to obtain complete coverage; (iii) identify the taxonomic affiliation of a metagenomic read or assembled contig; and (iv) determine differentially abundant genes, pathways, and species between different datasets. Most of these pipelines do not depend on the type of sequences available or can be easily adjusted to fit different types of sequences, and are freely available (for instance, through our lab Web site: http://www.enve-omics.gatech.edu/). The limitations of current approaches, as well as the computational aspects that can be further improved, will also be briefly discussed. The work presented here provides practical guidelines on how to perform metagenomic analysis of microbial communities characterized by varied levels of diversity and establishes approaches to handle the resulting data, independent of the sequencing platform employed. © 2013 Elsevier Inc. All rights reserved.

Effectiveness of exome and genome sequencing guided by acuity of illness for diagnosis of neurodevelopmental disorders

PubMed Central

Soden, Sarah E.; Saunders, Carol J.; Willig, Laurel K.; Farrow, Emily G.; Smith, Laurie D.; Petrikin, Josh E.; LePichon, Jean-Baptiste; Miller, Neil A.; Thiffault, Isabelle; Dinwiddie, Darrell L.; Twist, Greyson; Noll, Aaron; Heese, Bryce A.; Zellmer, Lee; Atherton, Andrea M.; Abdelmoity, Ahmed T.; Safina, Nicole; Nyp, Sarah S.; Zuccarelli, Britton; Larson, Ingrid A.; Modrcin, Ann; Herd, Suzanne; Creed, Mitchell; Ye, Zhaohui; Yuan, Xuan; Brodsky, Robert A.; Kingsmore, Stephen F.

2014-01-01

Neurodevelopmental disorders (NDDs) affect more than 3% of children and are attributable to single-gene mutations at more than 1000 loci. Traditional methods yield molecular diagnoses in less than one-half of children with NDD. Whole-genome sequencing (WGS) and whole-exome sequencing (WES) can enable diagnosis of NDD, but their clinical and cost-effectiveness are unknown. One hundred families with 119 children affected by NDD received diagnostic WGS and/or WES of parent-child trios, wherein the sequencing approach was guided by acuity of illness. Forty-five percent received molecular diagnoses. An accelerated sequencing modality, rapid WGS, yielded diagnoses in 73% of families with acutely ill children (11 of 15). Forty percent of families with children with nonacute NDD, followed in ambulatory care clinics (34 of 85), received diagnoses: 33 by WES and 1 by staged WES then WGS. The cost of prior negative tests in the nonacute patients was $19,100 per family, suggesting sequencing to be cost-effective at up to $7640 per family. A change in clinical care or impression of the pathophysiology was reported in 49% of newly diagnosed families. If WES or WGS had been performed at symptom onset, genomic diagnoses may have been made 77 months earlier than occurred in this study. It is suggested that initial diagnostic evaluation of children with NDD should include trio WGS or WES, with extension of accelerated sequencing modalities to high-acuity patients. PMID:25473036

Percutaneous coil embolization of massive pelvic pseudoaneurysm in an infant.

PubMed

Lillis, Anna P; Shaikh, Raja; Alomari, Ahmad I; Chaudry, Gulraiz

2015-06-01

Iatrogenic pseudoaneurysm formation is an uncommon but potentially serious complication of cardiac catheterization. This case report describes diagnosis and treatment of a large left external iliac artery pseudoaneurysm in a 3-month-old boy following cardiac catheterization and aortic balloon dilatation for aortic coarctation. A 4-cm pulsatile mass in the left hemipelvis was discovered on MRI performed 6 weeks later for possible tethered spinal cord. Sonography and angiography showed a large pseudoaneurysm of the left external iliac artery just distal to the iliac bifurcation with no flow in the external iliac artery distal to the pseudoaneurysm. Percutaneous US-guided thrombin injection was performed twice, with partial recanalization after each treatment. The residual portion of the pseudoaneurysm was then successfully embolized with percutaneous coils deployed under US and fluoroscopic guidance.

Child mortality in the Netherlands in the past decades: an overview of external causes and the role of public health policy.

PubMed

Gijzen, Sandra; Boere-Boonekamp, Magda M; L'Hoir, Monique P; Need, Ariana

2014-02-01

Among European countries, the Netherlands has the second lowest child mortality rate from external causes. We present an overview, discuss possible explanations, and suggest prevention measures. We analyzed mortality data from all deceased children aged 0-19 years for the period 1969-2011. Child mortality declined in the past decades, largely from decreases in road traffic accidents that followed government action on traffic safety. Accidental drowning also showed a downward trend. Although intentional self-harm showed a significant increase, other external causes of mortality, including assault and fatal child abuse, remained constant. Securing existing preventive measures and analyzing the circumstances of each child's death systematically through Child Death Review may guide further reduction in child mortality.

Ulysses Observations of Tripolar Guide-Magnetic Field Perturbations Across Solar Wind Reconnection Exhausts

NASA Astrophysics Data System (ADS)

Eriksson, S.; Peng, B.; Markidis, S.; Gosling, J. T.; McComas, D. J.; Lapenta, G.; Newman, D. L.

2014-12-01

We report observations from 15 solar wind reconnection exhausts encountered along the Ulysses orbit beyond 4 AU in 1996-1999 and 2002-2005. The events, which lasted between 17 and 45 min, were found at heliospheric latitudes between -36o and 21o with one event detected as high as 58o. All events shared a common characteristic of a tripolar guide-magnetic field perturbation being detected across the observed exhausts. The signature consists of an enhanced guide field magnitude within the exhaust center and two regions of significantly depressed guide-fields adjacent to the center region. The events displayed magnetic field shear angles as low as 37o with a mean of 89o. This corresponds to a strong external guide field relative to the anti-parallel reconnecting component of the magnetic field with a mean ratio of 1.3 and a maximum ratio of 3.1. A 2-D kinetic reconnection simulation for realistic solar wind conditions reveals that tripolar guide fields form at current sheets in the presence of multiple X-lines as two magnetic islands interact with one another for such strong guide fields. The Ulysses observations are also compared with the results of a 3-D kinetic simulation of multiple flux ropes in a strong guide field.

Differential Effects of Paced and Unpaced Responding on delayed Serial Order Recall in Schizophrenia

PubMed Central

Hill, S. Kristian; Griffin, Ginny B.; Houk, James C.; Sweeney, John A.

2011-01-01

Working memory for temporal order is a component of working memory that is especially dependent on striatal systems, but has not been extensively studied in schizophrenia. This study was designed to characterize serial order reproduction by adapting a spatial serial order task developed for nonhuman primate studies, while controlling for working memory load and whether responses were initiated freely (unpaced) or in an externally paced format. Clinically stable schizophrenia patients (n=27) and psychiatrically healthy individuals (n=25) were comparable on demographic variables and performance on standardized tests of immediate serial order recall (Digit Span, Spatial Span). No group differences were observed for serial order recall when read sequence reproduction was unpaced. However, schizophrenia patients exhibited significant impairments when responding was paced, regardless of sequence length or retention delay. Intact performance by schizophrenia patients during the unpaced condition indicates that prefrontal storage and striatal output systems are sufficiently intact to learn novel response sequences and hold them in working memory to perform serial order tasks. However, retention for newly learned response sequences was disrupted in schizophrenia patients by paced responding, when read-out of each element in the response sequence was externally controlled. The disruption of memory for serial order in paced read-out condition indicates a deficit in frontostriatal interaction characterized by an inability to update working memory stores and deconstruct ‘chunked’ information. PMID:21705197

Field guide to Cretaceous-tertiary boundary sections in northeastern Mexico

NASA Technical Reports Server (NTRS)

Keller, Gerta; Stinnesbeck, Wolfgang; Adatte, Thierry; Macleod, Norman; Lowe, Donald R.

1994-01-01

This guide was prepared for the field trip to the KT elastic sequence of northeastern Mexico, 5-8 February 1994, in conjunction with the Conference on New Developments Regarding the KT Event and Other Catastrophes in Earth History, held in Houston, Texas. The four-day excursion offers an invaluable opportunity to visit three key outcrops: Arroyo El Mimbral, La Lajilla, and El Pinon. These and other outcrops of this sequence have recently been interpreted as tsunami deposits produced by the meteorite impact event that produced the 200 to 300-km Chicxulub basin in Yucatan, and distributed ejecta around the world approximately 65 m.y. ago that today is recorded as a thin clay layer found at the K/T boundary. The impact tsunami interpretation for these rocks has not gone unchallenged, and others examining the outcrops arrive at quite different conclusions: not tsunami deposits but turbidites; not KT at all but 'upper Cretaceous.' Indeed, it is in hopes of resolving this debate through field discussion, outcrop evaluation, and sampling that led the organizers of the conference to sanction this field trip. This field guide provides participants with background information on the KT clastic sequence outcrops and is divided into two sections. The first section provides regional and logistical context for the outcrops and a description of the clastic sequence. The second section presents three representative interpretations of the outcrops by their advocates. There is clearly no way that these models can be reconciled and so two, if not all three, must be fundamentally wrong. Readers of this guide should keep in mind that many basic outcrop observations that these models are based upon remain unresolved. While great measures were taken to ensure that the information in the description section was as objective as possible, many observations are rooted in interpretations and the emphasis placed on certain observations depends to some degree upon the perspective of the author.

A method to synchronize signals from multiple patient monitoring devices through a single input channel for inclusion in list-mode acquisitions

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

O’Connor, J. Michael; Pretorius, P. Hendrik; Johnson, Karen

2013-12-15

Purpose: This technical note documents a method that the authors developed for combining a signal to synchronize a patient-monitoring device with a second physiological signal for inclusion into list-mode acquisition. Our specific application requires synchronizing an external patient motion-tracking system with a medical imaging system by multiplexing the tracking input with the ECG input. The authors believe that their methodology can be adapted for use in a variety of medical imaging modalities including single photon emission computed tomography (SPECT) and positron emission tomography (PET). Methods: The authors insert a unique pulse sequence into a single physiological input channel. This sequencemore » is then recorded in the list-mode acquisition along with the R-wave pulse used for ECG gating. The specific form of our pulse sequence allows for recognition of the time point being synchronized even when portions of the pulse sequence are lost due to collisions with R-wave pulses. This was achieved by altering our software used in binning the list-mode data to recognize even a portion of our pulse sequence. Limitations on heart rates at which our pulse sequence could be reliably detected were investigated by simulating the mixing of the two signals as a function of heart rate and time point during the cardiac cycle at which our pulse sequence is mixed with the cardiac signal. Results: The authors have successfully achieved accurate temporal synchronization of our motion-tracking system with acquisition of SPECT projections used in 17 recent clinical research cases. In our simulation analysis the authors determined that synchronization to enable compensation for body and respiratory motion could be achieved for heart rates up to 125 beats-per-minute (bpm). Conclusions: Synchronization of list-mode acquisition with external patient monitoring devices such as those employed in motion-tracking can reliably be achieved using a simple method that can be implemented using minimal external hardware and software modification through a single input channel, while still recording cardiac gating signals.« less

Precision global health in the digital age.

PubMed

Flahault, Antoine; Geissbuhler, Antoine; Guessous, Idris; Guérin, Philippe; Bolon, Isabelle; Salathé, Marcel; Escher, Gérard

2017-04-19

Precision global health is an approach similar to precision medicine, which facilitates, through innovation and technology, better targeting of public health interventions on a global scale, for the purpose of maximising their effectiveness and relevance. Illustrative examples include: the use of remote sensing data to fight vector-borne diseases; large databases of genomic sequences of foodborne pathogens helping to identify origins of outbreaks; social networks and internet search engines for tracking communicable diseases; cell phone data in humanitarian actions; drones to deliver healthcare services in remote and secluded areas. Open science and data sharing platforms are proposed for fostering international research programmes under fair, ethical and respectful conditions. Innovative education, such as massive open online courses or serious games, can promote wider access to training in public health and improving health literacy. The world is moving towards learning healthcare systems. Professionals are equipped with data collection and decision support devices. They share information, which are complemented by external sources, and analysed in real time using machine learning techniques. They allow for the early detection of anomalies, and eventually guide appropriate public health interventions. This article shows how information-driven approaches, enabled by digital technologies, can help improving global health with greater equity.

Interstitial and external radiotherapy in carcinoma of the soft palate and uvula

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

Esche, B.A.; Haie, C.M.; Gerbaulet, A.P.

1988-09-01

Forty-three patients, all male, with limited epidermoid carcinoma of the soft palate and uvula were treated by interstitial implant usually associated with external radiotherapy. Most patients received 50 Gy external irradiation to the oropharynx and neck followed by 20-35 Gy by interstitial iridium-192 wires using either guide gutters or a plastic tube technique. Twelve primary tumors and two recurrences after external irradiation alone had implant only for 65-75 Gy. Total actuarial local control is 92% with no local failures in 34 T1 primary tumors. Only one serious complication was seen. Overall actuarial survival was 60% at 3 years and 37%more » at 5 years but cause-specific survivals were 81% and 64%. The leading cause of death was other aerodigestive cancer, with an actuarial rate of occurrence of 10% per year after treatment of a soft palate cancer. Interstitital brachytherapy alone or combined with external irradiation is safe, effective management for early carcinoma of the soft palate and uvula but second malignancy is a serious problem.« less

Magnetically guiding and orienting integrated chemical sensors

NASA Astrophysics Data System (ADS)

Anker, Jeffrey N.; Lee, Yong-Eun Koo; Kopelman, Raoul

2014-08-01

Fluorescent microsensors for detecting pH and oxygen were positioned and oriented using magnetic tweezers. These multifunctional integrated microsensors were fabricated by physically linking together nano-components including magnetic nanoparticles, fluorescent nanoparticles, and metal hemisphere-shells. Two such microsensors are magnetic roll-shaped polystyrene particles with 120 nm fluorescent oxygen-sensing ormosil nanospheres that are physically pressed ("breaded") into the roll surface, and 4-5 µm fluorescent microspheres that are capped with a 50 nm thick metal hemispherical shell. The magnetic tweezers consisted of an iron wire that was magnetized in an external magnetic field. Rotating this external field oriented and rotated the microsensors.

Latching micro optical switch

DOEpatents

Garcia, Ernest J; Polosky, Marc A

2013-05-21

An optical switch reliably maintains its on or off state even when subjected to environments where the switch is bumped or otherwise moved. In addition, the optical switch maintains its on or off state indefinitely without requiring external power. External power is used only to transition the switch from one state to the other. The optical switch is configured with a fixed optical fiber and a movable optical fiber. The movable optical fiber is guided by various actuators in conjunction with a latching mechanism that configure the switch in one position that corresponds to the on state and in another position that corresponds to the off state.

Sunshine School's S.O.P.: Sequenced Objectives for Preschoolers. An Evaluation and Instruction Guide for Working with the Developmentally Delayed.

ERIC Educational Resources Information Center

Sunshine School, Gainesville, FL.

Developed by professional educational staff, the curriculum of developmentally sequenced objectives for preschoolers (SOP) is designed for use in infant stimulation programs, for preschool training for all levels of retardation, with severely and profoundly retarded school age children, and for trainable and educable children during the earlier…

Physics First: An Informational Guide for Teachers, School Administrators, Parents, Scientists, and the Public

ERIC Educational Resources Information Center

American Association of Physics Teachers (NJ1), 2009

2009-01-01

Physics First represents an organizational alternative to the traditional high school science sequence. It calls for a re-sequencing of high school courses so that students study physics before chemistry and biology. The purpose of this pamphlet is to provide: (1) Basic information and rationale for the Physics First curriculum; (2) Strategies for…

Sludge Lagoons. Sludge Treatment and Disposal Course #166. Instructor's Guide [and] Student Workbook.

ERIC Educational Resources Information Center

Sharman, Ronald M.

This lesson describes three different types of sludge lagoons: (1) drying lagoons; (2) facultative lagoons; and (3) anaerobic lagoons. Normal operating sequence and equipment are also described. The lesson is designed to be used in sequence with the complete Sludge Treatment and Disposal Course #166 or as an independent lesson. The instructor's…

A Guide to Analyzing Message-Response Sequences and Group Interaction Patterns in Computer-Mediated Communication

ERIC Educational Resources Information Center

Jeong, Allan

2005-01-01

This paper proposes a set of methods and a framework for evaluating, modeling, and predicting group interactions in computer-mediated communication. The method of sequential analysis is described along with specific software tools and techniques to facilitate the analysis of message-response sequences. In addition, the Dialogic Theory and its…

Planning a Teaching Sequence for the Teaching of Chemical Bonding

ERIC Educational Resources Information Center

Sibanda, Doras; Hobden, Paul

2015-01-01

The current study seeks to examine how teachers plan teaching sequences to teach chemical bonding in the senior secondary phase of schooling. The study employs a learning demand tool as interpretive framework. A mixed method was used to guide the collection of data. Data were collected through a survey instrument with 227 practising physical…

BASINS and WEPP Climate Assessment Tools (CAT): Case Study Guide to Potential Applications (External Review Draft)

EPA Science Inventory

This draft report supports application of two recently developed water modeling tools, the BASINS and WEPP climate assessment tools. The report presents a series of short case studies designed to illustrate the capabilities of these tools for conducting scenario based assessments...

Grantee :: NOAA Acquisition and Grants Office

Science.gov Websites

Guide AGO Systems C.Suite C.Request C.Award FPDS-NG SAM FAAPS CPARS eSRS Training COR Procurement Policy Training Forms External Links Grantee Policy DOC Grants and Cooperative Agreements Regulations Grants Online Grants Online Training Automated Standard Application for Payment (ASAP) - Grantee

University of Maryland MRSEC - Research: Seed 3

Science.gov Websites

MRSEC Templates Opportunities Search Home » Research » Seed 3 Seed 3: Modeling Elastic Effects on controlling parameters and variables include temperature, deposition flux, external electric field and elastic simulating the effects of these controlling factors often lead to predictions that guide future experiments

The Research Funding Guidebook: Getting It, Managing It, and Renewing It.

ERIC Educational Resources Information Center

Ries, Joanne B.; Leukefeld, Carl G.

This guide, intended primarily for new or inexperienced researchers, provides suggestions for obtaining and maintaining external funding from grants and contracts. It emphasizes that this effort requires considerable thought, ongoing planning, sound management, and clear decisions. The book uses the National Institutes of Health application and…

Insights into university freshman weight issues and how they make decisions about eating

USDA-ARS?s Scientific Manuscript database

The transition from high school to college represents a turning point during which health behavior trajectories may be influenced. This study addresses the internal and external factors that guide students’ eating decisions as they are understood and relayed by students through ethnographic, qualit...

Knowledge Creation through User-Guided Data Mining: A Database Case

ERIC Educational Resources Information Center

Steiger, David M.

2008-01-01

This case focuses on learning by applying the four integrating mechanisms of Nonaka's knowledge creation theory: socialization, externalization, combination and internalization. In general, such knowledge creation and internalization (i.e., learning) is critical to database students since they will be expected to apply their specialized database…

Teacher Evaluation Policy and Conflicting Theories of Motivation

ERIC Educational Resources Information Center

Firestone, William A.

2014-01-01

Current interest in teacher evaluation focuses disproportionately on measurement issues and performance-based pay without an overarching theory of how evaluation works. To develop such a theory, I contrast two motivation theories often used to guide thinking about teacher evaluation. External motivation theory relies on economics and extrinsic…

Mixed Ability Teaching: Meeting Learners' Needs. Netword 3: Teaching Languages to Adults.

ERIC Educational Resources Information Center

Ainslie, Susan

This guide, designed for teachers of second languages to adults, discusses instruction for student groups of mixed abilities. The first chapter examines the factors that determine mixed ability, including: student motivation, interests, and needs; linguistic ability; general educational background; learning style; age; external pressures and time…

SU-F-E-02: A Feasibility Study for Application of Metal Artifact Reduction Techniques in MR-Guided Brachytherapy Gynecological Cancer with Titanium Applicators

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

Kadbi, M

Purpose: Utilization of Titanium Tandem and Ring (T&R) applicators in MR-guided brachytherapy has become widespread for gynecological cancer treatment. However, Titanium causes magnetic field disturbance and susceptibility artifact, which complicate image interpretation. In this study, metal artifact reduction techniques were employed to improve the image quality and reduce the metal related artifacts. Methods: Several techniques were employed to reduce the metal artifact caused by titanium T&R applicator. These techniques include Metal Artifact Reduction Sequence (MARS), View Angle Tilting (VAT) to correct in-plane distortion, and Slice Encoding for Metal Artifact Correction (SEMAC) for through-plane artifact correction. Moreover, MARS can be combinedmore » with VAT to further reduce the in-plane artifact by reapplying the selection gradients during the readout (MARS+VAT). SEMAC uses a slice selective excitation but acquires additional z-encodings in order to resolve off-resonant signal and to reduce through-plane distortions. Results: Comparison between the clinical sequences revealed that increasing the bandwidth reduces the error in measured diameter of T&R. However, the error is larger than 4mm for the best case with highest bandwidth and spatial resolution. MARS+VAT with isotropic resolution of 1mm reduced the error to 1.9mm which is the least among the examined 2D sequences. The measured diameter of tandem from SEMAC+VAT has the closest value to the actual diameter of tandem (3.2mm) and the error was reduced to less than 1mm. In addition, SEMAC+VAT significantly reduces the blooming artifact in the ring compared to clinical sequences. Conclusion: A higher bandwidth and spatial resolution sequence reduces the artifact and diameter of applicator with a slight compromise in SNR. Metal artifact reduction sequences decrease the distortion associated with titanium applicator. SEMAC+VAT sequence in combination with VAT revealed promising results for titanium imaging and can be utilized for MR-guided brachytherapy in gynecological cancer. The author is employee with Philips Healthcare.« less

StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees.

PubMed

Roosaare, Märt; Vaher, Mihkel; Kaplinski, Lauris; Möls, Märt; Andreson, Reidar; Lepamets, Maarja; Kõressaar, Triinu; Naaber, Paul; Kõljalg, Siiri; Remm, Maido

2017-01-01

Fast, accurate and high-throughput identification of bacterial isolates is in great demand. The present work was conducted to investigate the possibility of identifying isolates from unassembled next-generation sequencing reads using custom-made guide trees. A tool named StrainSeeker was developed that constructs a list of specific k -mers for each node of any given Newick-format tree and enables the identification of bacterial isolates in 1-2 min. It uses a novel algorithm, which analyses the observed and expected fractions of node-specific k -mers to test the presence of each node in the sample. This allows StrainSeeker to determine where the isolate branches off the guide tree and assign it to a clade whereas other tools assign each read to a reference genome. Using a dataset of 100 Escherichia coli isolates, we demonstrate that StrainSeeker can predict the clades of E. coli with 92% accuracy and correct tree branch assignment with 98% accuracy. Twenty-five thousand Illumina HiSeq reads are sufficient for identification of the strain. StrainSeeker is a software program that identifies bacterial isolates by assigning them to nodes or leaves of a custom-made guide tree. StrainSeeker's web interface and pre-computed guide trees are available at http://bioinfo.ut.ee/strainseeker. Source code is stored at GitHub: https://github.com/bioinfo-ut/StrainSeeker.

Epigenomics

MedlinePlus

... Sheets A Brief Guide to Genomics About NHGRI Research About the International HapMap Project Biological Pathways Chromosome Abnormalities Chromosomes Cloning Comparative Genomics DNA Microarray Technology DNA Sequencing Deoxyribonucleic Acid ( ...

Cloning

MedlinePlus

... Sheets A Brief Guide to Genomics About NHGRI Research About the International HapMap Project Biological Pathways Chromosome Abnormalities Chromosomes Cloning Comparative Genomics DNA Microarray Technology DNA Sequencing Deoxyribonucleic Acid ( ...

Chromosomes

MedlinePlus

... Sheets A Brief Guide to Genomics About NHGRI Research About the International HapMap Project Biological Pathways Chromosome Abnormalities Chromosomes Cloning Comparative Genomics DNA Microarray Technology DNA Sequencing Deoxyribonucleic Acid ( ...

Transcriptome

MedlinePlus

... Sheets A Brief Guide to Genomics About NHGRI Research About the International HapMap Project Biological Pathways Chromosome Abnormalities Chromosomes Cloning Comparative Genomics DNA Microarray Technology DNA Sequencing Deoxyribonucleic Acid ( ...

Comparison of delayed complications of central venous catheters placed surgically or radiologically in pediatric oncology patients.

PubMed

Basford, Tavis J; Poenaru, Dan; Silva, Mariana

2003-05-01

Pediatric central venous catheters (CVCs) traditionally have been placed surgically, guided by anatomic landmarks. Increasingly, interventional radiology services are inserting CVCs using ultrasound image guidance. This study compares the frequency of delayed complications in CVCs placed surgically or radiologically in a pediatric oncology population. Data on CVCs placed in one academic institution over 10 years were collected and analyzed retrospectively. Main outcomes assessed were infectious complications, mechanical complications, and premature catheter removal. Ninety-eight CVCs-comprising 52 external tunneled catheters (ETCs) and 46 subcutaneous ports-were assessed in 67 patients. Median patient age was 6.1 years for children with external catheters and 7.8 years for those with ports. Both infectious and mechanical complications were significantly more common among surgically placed ETCs than those placed radiologically (P <.05). Complications per 1,000 catheter days and premature removal showed a trend toward greater frequency among surgical ETCs, although this did not reach statistical significance. No consistent trends were seen in complications among ports. Pediatric patients with CVCs, especially those with external catheters, experience frequent delayed complications. Patients with radiologically inserted ETCs may encounter fewer complications than those with surgically placed ones. This corroborates previous reports in the literature suggesting image-guided CVC placement as a preferable alternative to traditional techniques. Copyright 2003 Elsevier Inc. All rights reserved.

Cloning and Identification of Recombinant Argonaute-Bound Small RNAs Using Next-Generation Sequencing.

PubMed

Gangras, Pooja; Dayeh, Daniel M; Mabin, Justin W; Nakanishi, Kotaro; Singh, Guramrit

2018-01-01

Argonaute proteins (AGOs) are loaded with small RNAs as guides to recognize target mRNAs. Since the target specificity heavily depends on the base complementarity between two strands, it is important to identify small guide and long target RNAs bound to AGOs. For this purpose, next-generation sequencing (NGS) technologies have extended our appreciation truly to the nucleotide level. However, the identification of RNAs via NGS from scarce RNA samples remains a challenge. Further, most commercial and published methods are compatible with either small RNAs or long RNAs, but are not equally applicable to both. Therefore, a single method that yields quantitative, bias-free NGS libraries to identify small and long RNAs from low levels of input will be of wide interest. Here, we introduce such a procedure that is based on several modifications of two published protocols and allows robust, sensitive, and reproducible cloning and sequencing of small amounts of RNAs of variable lengths. The method was applied to the identification of small RNAs bound to a purified eukaryotic AGO. Following ligation of a DNA adapter to RNA 3'-end, the key feature of this method is to use the adapter for priming reverse transcription (RT) wherein biotinylated deoxyribonucleotides specifically incorporated into the extended complementary DNA. Such RT products are enriched on streptavidin beads, circularized while immobilized on beads and directly used for PCR amplification. We provide a stepwise guide to generate RNA-Seq libraries, their purification, quantification, validation, and preparation for next-generation sequencing. We also provide basic steps in post-NGS data analyses using Galaxy, an open-source, web-based platform.

Genetic Mapping

MedlinePlus

... Sheets A Brief Guide to Genomics About NHGRI Research About the International HapMap Project Biological Pathways Chromosome Abnormalities Chromosomes Cloning Comparative Genomics DNA Microarray Technology DNA Sequencing Deoxyribonucleic Acid ( ...

Biological Pathways

MedlinePlus

... Sheets A Brief Guide to Genomics About NHGRI Research About the International HapMap Project Biological Pathways Chromosome Abnormalities Chromosomes Cloning Comparative Genomics DNA Microarray Technology DNA Sequencing Deoxyribonucleic Acid ( ...

Tour Recommendation Guide- Personalized travel sequence recommendation

NASA Astrophysics Data System (ADS)

Sivakumar, Akshitha; Prabadevi, B.

2017-11-01

Presents a personalized travel sequence for the given area the individual wants to visit. It not only helps to personalize the travel but also recommend a travel sequence based on the area mentioned. Firstly the frequently visited routes are ranked then top ranked routes are chosen based on previous travel records. The data is being collected using data mining and the famous routes are ranked based on user and the route. It helps in bridging the gap between user travel preference and routes.

a Continuous Health Monitoring Guided Wave Fmd System for Retrofit to Existing Offshore Oilrigs

NASA Astrophysics Data System (ADS)

Mijarez, R.; Solis, L.; Martinez, F.

2010-02-01

An automatic health monitoring guided wave flood member detection (FMD) system, for retrofit to existing offshore oilrigs is presented. The system employs a microcontroller piezoelectric (PZT) based transmitter and a receiver instrumentation package composed of a PZT 40 kHz ultrasound transducer and a digital signal processor (DSP) module connected to a PC via USB for monitoring purposes. The transmitter and receiver were attached, non-intrusively, to the external wall of a steel tube; 1 m×27 cm×2 mm. Experiments performed in the laboratory have successfully identified automatically flooded tubes.

Resonance-enhanced optical forces between coupled photonic crystal slabs.

PubMed

Liu, Victor; Povinelli, Michelle; Fan, Shanhui

2009-11-23

The behaviors of lateral and normal optical forces between coupled photonic crystal slabs are analyzed. We show that the optical force is periodic with displacement, resulting in stable and unstable equilibrium positions. Moreover, the forces are strongly enhanced by guided resonances of the coupled slabs. Such enhancement is particularly prominent near dark states of the system, and the enhancement effect is strongly dependent on the types of guided resonances involved. These structures lead to enhancement of light-induced pressure over larger areas, in a configuration that is directly accessible to externally incident, free-space optical beams.

Chemistry of Living Matter, Energy Capture & Growth, Parts Three & Four of an Integrated Science Sequence, Student Guide, 1971 Edition.

ERIC Educational Resources Information Center

Portland Project Committee, OR.

This student guide is divided into two sections, "Chemistry of Living Matter" and "Energy Capture and Growth," constituting parts three and four of the third year of the Portland Project, a three-year high school integrated science curriculum. The underlying intention of the third year is to study energy and its importance to…

Motion and Energy Chemical Reactions, Parts One & Two of an Integrated Science Sequence, Student Guide, 1971 Edition.

ERIC Educational Resources Information Center

Portland Project Committee, OR.

This student guide is for the second year of the Portland Project, a three-year integrated secondary school science curriculum. "Motion and Energy," the first of the two parts in this volume, begins with the study of motion, going from the quantitative description of motion to a consideration of what causes motion and a discussion of…

Iron oxide nanoparticles for magnetically-guided and magnetically-responsive drug delivery.

PubMed

Estelrich, Joan; Escribano, Elvira; Queralt, Josep; Busquets, Maria Antònia

2015-04-10

In this review, we discuss the recent advances in and problems with the use of magnetically-guided and magnetically-responsive nanoparticles in drug delivery and magnetofection. In magnetically-guided nanoparticles, a constant external magnetic field is used to transport magnetic nanoparticles loaded with drugs to a specific site within the body or to increase the transfection capacity. Magnetofection is the delivery of nucleic acids under the influence of a magnetic field acting on nucleic acid vectors that are associated with magnetic nanoparticles. In magnetically-responsive nanoparticles, magnetic nanoparticles are encapsulated or embedded in a larger colloidal structure that carries a drug. In this last case, an alternating magnetic field can modify the structure of the colloid, thereby providing spatial and temporal control over drug release.

Iron Oxide Nanoparticles for Magnetically-Guided and Magnetically-Responsive Drug Delivery

PubMed Central

Estelrich, Joan; Escribano, Elvira; Queralt, Josep; Busquets, Maria Antònia

2015-01-01

In this review, we discuss the recent advances in and problems with the use of magnetically-guided and magnetically-responsive nanoparticles in drug delivery and magnetofection. In magnetically-guided nanoparticles, a constant external magnetic field is used to transport magnetic nanoparticles loaded with drugs to a specific site within the body or to increase the transfection capacity. Magnetofection is the delivery of nucleic acids under the influence of a magnetic field acting on nucleic acid vectors that are associated with magnetic nanoparticles. In magnetically-responsive nanoparticles, magnetic nanoparticles are encapsulated or embedded in a larger colloidal structure that carries a drug. In this last case, an alternating magnetic field can modify the structure of the colloid, thereby providing spatial and temporal control over drug release. PMID:25867479

The utility of vignettes to stimulate reflection on professionalism: theory and practice.

PubMed

Bernabeo, E C; Holmboe, E S; Ross, K; Chesluk, B; Ginsburg, S

2013-08-01

Professionalism remains a substantive theme in medical literature. There is an emerging emphasis on sociological and complex adaptive systems perspectives that refocuses attention from just the individual role to working within one's system to enact professionalism in practice. Reflecting on responses to professional dilemmas may be one method to help practicing physicians identify both internal and external factors contributing to (un) professional behavior. We present a rationale and theoretical framework that supports and guides a reflective approach to the self assessment of professionalism. Guided by principles grounded in this theoretical framework, we developed and piloted a set of vignettes on professionally challenging situations, designed to stimulate reflection in practicing physicians. Findings show that participants found the vignettes to be authentic and typical, and reported the group experience as facilitative around discussions of professional ambiguity. Providing an opportunity for physicians to reflect on professional behavior in an open and safe forum may be a practical way to guide physicians to assess themselves on professional behavior and engage with the complexities of their work. The finding that the focus groups led to reflection at a group level suggests that effective reflection on professional behavior may require a socially interactive process. Emphasizing both the behaviors and the internal and external context in which they occur can thus be viewed as critically important for understanding professionalism in practicing physicians.

Endoluminal MR-guided ultrasonic applicator embedding cylindrical phased-array transducers and opposed-solenoid detection coil.

PubMed

Rata, Mihaela; Birlea, Vlad; Murillo, Adriana; Paquet, Christian; Cotton, François; Salomir, Rares

2015-01-01

MR-guided high-intensity contact ultrasound (HICU) was suggested as an alternative therapy for esophageal and rectal cancer. To offer high-quality MR guidance, two prototypes of receive-only opposed-solenoid coil were integrated with 64-element cylindrical phased-array ultrasound transducers (rectal/esophageal). The design of integrated coils took into account the transducer geometry (360° acoustic window within endoluminal space). The rectal coil was sealed on a plastic support and placed reversibly on the transducer head. The esophageal coil was fully embedded within the transducer head, resulting in one indivisible device. Comparison of integrated versus external coils was performed on a clinical 1.5T scanner. The integrated coils showed higher sensitivity compared with the standard extracorporeal coil with factors of up to 7.5 (rectal applicator) and 3.3 (esophageal applicator). High-resolution MR images for both anatomy (voxel 0.4 × 0.4 × 5 mm(3)) and thermometry (voxel 0.75 × 0.75 × 8 mm(3), 2 s/image) were acquired in vivo with the rectal endoscopic device. The temperature feedback loop accurately controlled multiple control points over the region of interest. This study showed significant improvement of MR data quality using endoluminal integrated coils versus standard external coil. Inframillimeter spatial resolution and accurate feedback control of MR-guided HICU thermotherapy were achieved. © 2014 Wiley Periodicals, Inc.

Phospholipid micelle-based magneto-plasmonic nanoformulation for magnetic field-directed, imaging-guided photo-induced cancer therapy.

PubMed

Ohulchanskyy, Tymish Y; Kopwitthaya, Atcha; Jeon, Mansik; Guo, Moran; Law, Wing-Cheung; Furlani, Edward P; Kim, Chulhong; Prasad, Paras N

2013-11-01

We present a magnetoplasmonic nanoplatform combining gold nanorods (GNR) and iron-oxide nanoparticles within phospholipid-based polymeric nanomicelles (PGRFe). The gold nanorods exhibit plasmon resonance absorbance at near infrared wavelengths to enable photoacoustic imaging and photothermal therapy, while the Fe3O4 nanoparticles enable magnetophoretic control of the nanoformulation. The fabricated nanoformulation can be directed and concentrated by an external magnetic field, which provides enhancement of a photoacoustic signal. Application of an external field also leads to enhanced uptake of the magnetoplasmonic formulation by cancer cells in vitro. Under laser irradiation at the wavelength of the GNR absorption peak, the PGRFe formulation efficiently generates plasmonic nanobubbles within cancer cells, as visualized by confocal microscopy, causing cell destruction. The combined magnetic and plasmonic functionalities of the nanoplatform enable magnetic field-directed, imaging-guided, enhanced photo-induced cancer therapy. In this study, a nano-formulation of gold nanorods and iron oxide nanoparticles is presented using a phospholipid micelle-based delivery system for magnetic field-directed and imaging-guided photo-induced cancer therapy. The gold nanorods enable photoacoustic imaging and photothermal therapy, while the Fe3O4 nanoparticles enable magnetophoretic control of the formulation. This and similar systems could enable more precise and efficient cancer therapy, hopefully in the near future, after additional testing. Copyright © 2013 Elsevier Inc. All rights reserved.

Innovation in the imaging perianal fistula: a step towards personalised medicine

PubMed Central

Sahnan, Kapil; Adegbola, Samuel O.; Tozer, Philip J.; Patel, Uday; Ilangovan, Rajpandian; Warusavitarne, Janindra; Faiz, Omar D.; Hart, Ailsa L.; Phillips, Robin K. S.; Lung, Phillip F. C.

2018-01-01

Background: Perianal fistula is a topic both hard to understand and to teach. The key to understanding the treatment options and the likely success is deciphering the exact morphology of the tract(s) and the amount of sphincter involved. Our aim was to explore alternative platforms better to understand complex perianal fistulas through three-dimensional (3D) imaging and reconstruction. Methods: Digital imaging and communications in medicine images of spectral attenuated inversion recovery magnetic resonance imaging (MRI) sequences were imported onto validated open-source segmentation software. A specialist consultant gastrointestinal radiologist performed segmentation of the fistula, internal and external sphincter. Segmented files were exported as stereolithography files. Cura (Ultimaker Cura 3.0.4) was used to prepare the files for printing on an Ultimaker 3 Extended 3D printer. Animations were created in collaboration with Touch Surgery™. Results: Three examples of 3D printed models demonstrating complex perianal fistula were created. The anatomical components are displayed in different colours: red: fistula tract; green: external anal sphincter and levator plate; blue: internal anal sphincter and rectum. One of the models was created to be split in half, to display the internal opening and allow complexity in the intersphincteric space to better evaluated. An animation of MRI fistulography of a trans-sphincteric fistula tract with a cephalad extension in the intersphincteric space was also created. Conclusion: MRI is the reference standard for assessment of perianal fistula, defining anatomy and guiding surgery. However, communication of findings between radiologist and surgeon remains challenging. Feasibility of 3D reconstructions of complex perianal fistula is realized, with the potential to improve surgical planning, communication with patients, and augment training. PMID:29854001

Understanding the Stress Process of Chinese- and Korean-American Breast Cancer Survivors

PubMed Central

Lim, Jung-won

2017-01-01

Guided by the stress process model (SPM), this study investigated the direct and indirect pathways of primary (negative self-image and life stress), secondary stressors (family communication strain) and family coping (external and internal) on mental health outcomes among Chinese- and Korean-American breast cancer survivors (BCS). A total of 156 Chinese- and Korean-American BCS were surveyed. Results showed primary and secondary stressors had a negative effect on better mental health outcomes. External coping was associated with better mental health. Family communication strain mediated the relationship between life stress and mental health outcomes. External coping mediated the relationship between family communication strain and mental health outcomes. Multi-group analysis revealed the stress process did not differ across ethnic groups. Findings suggest the SPM may be applicable to understand the stress process of Chinese-and Korean-American BCS and provide valuable insight into the role of family communication and external coping on mental health outcomes. PMID:26223968

Diffusion of external magnetic fields into the cone-in-shell target in the fast ignition

NASA Astrophysics Data System (ADS)

Sunahara, Atsushi; Morita, Hiroki; Johzaki, Tomoyuki; Nagatomo, Hideo; Fujioka, Shinsuke; Hassanein, Ahmed; Firex Project Team

2017-10-01

We simulated the diffusion of externally applied magnetic fields into cone-in-shell target in the fast ignition. Recently, in the fast ignition scheme, the externally magnetic fields up to kilo-Tesla is used to guide fast electrons to the high-dense imploded core. In order to study the profile of the magnetic field, we have developed 2D cylindrical Maxwell equation solver with Ohm's law, and carried out simulations of diffusion of externally applied magnetic fields into a cone-in-shell target. We estimated the conductivity of the cone and shell target based on the assumption of Saha-ionization equilibrium. Also, we calculated the temporal evolution of the target temperature heated by the eddy current driven by temporal variation of magnetic fields, based on the accurate equation of state. Both, the diffusion of magnetic field and the increase of target temperature interact with each other. We present our results of temporal evolution of the magnetic field and its diffusion into the cone and shell target.

Airworthiness Qualification Criteria for Rotorcraft with External Sling Loads

NASA Technical Reports Server (NTRS)

Key, David L.

2002-01-01

This report presents the results of a study to develop airworthiness requirements for rotorcraft with external sling loads. The report starts with a review of the various phenomena that limit external sling load operations. Specifically discussed are the rotorcraft-load aeroservoelastic stability, load-on handling qualities, effects of automatic flight control system failure, load suspension system failure, and load stability at speed. Based on past experience and treatment of these phenomena, criteria are proposed to form a package for airworthiness qualification. The desired end objective is a set of operational flight envelopes for the rotorcraft with intended loads that can be provided to the user to guide operations in the field. The specific criteria proposed are parts of ADS-33E-PRF; MIL-F-9490D, and MIL-STD-913A all applied in the context of external sling loads. The study was performed for the Directorate of Engineering, U.S. Army Aviation and Missile Command (AMCOM), as part of the contract monitored by the Aerothermodynamics Directorate, U.S. Army AMCOM.

Newton's method: A link between continuous and discrete solutions of nonlinear problems

NASA Technical Reports Server (NTRS)

Thurston, G. A.

1980-01-01

Newton's method for nonlinear mechanics problems replaces the governing nonlinear equations by an iterative sequence of linear equations. When the linear equations are linear differential equations, the equations are usually solved by numerical methods. The iterative sequence in Newton's method can exhibit poor convergence properties when the nonlinear problem has multiple solutions for a fixed set of parameters, unless the iterative sequences are aimed at solving for each solution separately. The theory of the linear differential operators is often a better guide for solution strategies in applying Newton's method than the theory of linear algebra associated with the numerical analogs of the differential operators. In fact, the theory for the differential operators can suggest the choice of numerical linear operators. In this paper the method of variation of parameters from the theory of linear ordinary differential equations is examined in detail in the context of Newton's method to demonstrate how it might be used as a guide for numerical solutions.

Chromatin accessibility and guide sequence secondary structure affect CRISPR-Cas9 gene editing efficiency.

PubMed

Jensen, Kristopher Torp; Fløe, Lasse; Petersen, Trine Skov; Huang, Jinrong; Xu, Fengping; Bolund, Lars; Luo, Yonglun; Lin, Lin

2017-07-01

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated protein 9 (CRISPR-Cas9) systems have emerged as the method of choice for genome editing, but large variations in on-target efficiencies continue to limit their applicability. Here, we investigate the effect of chromatin accessibility on Cas9-mediated gene editing efficiency for 20 gRNAs targeting 10 genomic loci in HEK293T cells using both SpCas9 and the eSpCas9(1.1) variant. Our study indicates that gene editing is more efficient in euchromatin than in heterochromatin, and we validate this finding in HeLa cells and in human fibroblasts. Furthermore, we investigate the gRNA sequence determinants of CRISPR-Cas9 activity using a surrogate reporter system and find that the efficiency of Cas9-mediated gene editing is dependent on guide sequence secondary structure formation. This knowledge can aid in the further improvement of tools for gRNA design. © 2017 Federation of European Biochemical Societies.

Mutations in Cas9 Enhance the Rate of Acquisition of Viral Spacer Sequences during the CRISPR-Cas Immune Response.

PubMed

Heler, Robert; Wright, Addison V; Vucelja, Marija; Bikard, David; Doudna, Jennifer A; Marraffini, Luciano A

2017-01-05

CRISPR loci and their associated (Cas) proteins encode a prokaryotic immune system that protects against viruses and plasmids. Upon infection, a low fraction of cells acquire short DNA sequences from the invader. These sequences (spacers) are integrated in between the repeats of the CRISPR locus and immunize the host against the matching invader. Spacers specify the targets of the CRISPR immune response through transcription into short RNA guides that direct Cas nucleases to the invading DNA molecules. Here we performed random mutagenesis of the RNA-guided Cas9 nuclease to look for variants that provide enhanced immunity against viral infection. We identified a mutation, I473F, that increases the rate of spacer acquisition by more than two orders of magnitude. Our results highlight the role of Cas9 during CRISPR immunization and provide a useful tool to study this rare process and develop it as a biotechnological application. Copyright © 2017 Elsevier Inc. All rights reserved.

International Interlaboratory Digital PCR Study Demonstrating High Reproducibility for the Measurement of a Rare Sequence Variant.

PubMed

Whale, Alexandra S; Devonshire, Alison S; Karlin-Neumann, George; Regan, Jack; Javier, Leanne; Cowen, Simon; Fernandez-Gonzalez, Ana; Jones, Gerwyn M; Redshaw, Nicholas; Beck, Julia; Berger, Andreas W; Combaret, Valérie; Dahl Kjersgaard, Nina; Davis, Lisa; Fina, Frederic; Forshew, Tim; Fredslund Andersen, Rikke; Galbiati, Silvia; González Hernández, Álvaro; Haynes, Charles A; Janku, Filip; Lacave, Roger; Lee, Justin; Mistry, Vilas; Pender, Alexandra; Pradines, Anne; Proudhon, Charlotte; Saal, Lao H; Stieglitz, Elliot; Ulrich, Bryan; Foy, Carole A; Parkes, Helen; Tzonev, Svilen; Huggett, Jim F

2017-02-07

This study tested the claim that digital PCR (dPCR) can offer highly reproducible quantitative measurements in disparate laboratories. Twenty-one laboratories measured four blinded samples containing different quantities of a KRAS fragment encoding G12D, an important genetic marker for guiding therapy of certain cancers. This marker is challenging to quantify reproducibly using quantitative PCR (qPCR) or next generation sequencing (NGS) due to the presence of competing wild type sequences and the need for calibration. Using dPCR, 18 laboratories were able to quantify the G12D marker within 12% of each other in all samples. Three laboratories appeared to measure consistently outlying results; however, proper application of a follow-up analysis recommendation rectified their data. Our findings show that dPCR has demonstrable reproducibility across a large number of laboratories without calibration. This could enable the reproducible application of molecular stratification to guide therapy and, potentially, for molecular diagnostics.

Female pseudohermaphroditism with multiple caudal anomalies: Absence of Y-specific DNA sequences as pathogenetic factors

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

Seaver, L.H.; Grimes, J.; Erickson, R.P.

1994-05-15

46,XX female pseudohermaphrodites have been previously described with nearly complete masculinization of the external genitalia and no apparent source of testosterone. Multiple malformations of internal genital, urinary, and gastrointestinal tracts are associated. We have evaluated four such infants with female pseudohermaphroditism and multiple caudal anomalies. Three cases had apparently normal chromosome (46,XX); one had a 46,XX,del(10)(q25.3{yields}qter) chromosome constitution. The chromosome breakpoint is in the region of PAX2, a developmentally important paired box gene which is expressed in urogenital tissue. Using the polymerase chain reaction, we screened for the presence of multiple Y specific sequences, including SRY (sex determining region, Ymore » chromosome), that could explain masculinization of the external genitalia. All were negative for Y centromeric sequences, ZFY (Zinc finger Y), and SRY. Furthermore, there was no evidence for adrenal or other sources of testosterone. We suggest that the masculinization in these cases is the result of abnormal expression of genes which would normally be regulated by testosterone. 32 refs., 1 fig., 2 tabs.« less

Hybrid computing using a neural network with dynamic external memory.

PubMed

Graves, Alex; Wayne, Greg; Reynolds, Malcolm; Harley, Tim; Danihelka, Ivo; Grabska-Barwińska, Agnieszka; Colmenarejo, Sergio Gómez; Grefenstette, Edward; Ramalho, Tiago; Agapiou, John; Badia, Adrià Puigdomènech; Hermann, Karl Moritz; Zwols, Yori; Ostrovski, Georg; Cain, Adam; King, Helen; Summerfield, Christopher; Blunsom, Phil; Kavukcuoglu, Koray; Hassabis, Demis

2016-10-27

Artificial neural networks are remarkably adept at sensory processing, sequence learning and reinforcement learning, but are limited in their ability to represent variables and data structures and to store data over long timescales, owing to the lack of an external memory. Here we introduce a machine learning model called a differentiable neural computer (DNC), which consists of a neural network that can read from and write to an external memory matrix, analogous to the random-access memory in a conventional computer. Like a conventional computer, it can use its memory to represent and manipulate complex data structures, but, like a neural network, it can learn to do so from data. When trained with supervised learning, we demonstrate that a DNC can successfully answer synthetic questions designed to emulate reasoning and inference problems in natural language. We show that it can learn tasks such as finding the shortest path between specified points and inferring the missing links in randomly generated graphs, and then generalize these tasks to specific graphs such as transport networks and family trees. When trained with reinforcement learning, a DNC can complete a moving blocks puzzle in which changing goals are specified by sequences of symbols. Taken together, our results demonstrate that DNCs have the capacity to solve complex, structured tasks that are inaccessible to neural networks without external read-write memory.

Single shot FASTBUS sequencer

NASA Astrophysics Data System (ADS)

Ikeda, H.

1989-10-01

A description is given of a single-shot sequencer, a FASTBUS master module that can execute only a predetermined FASTBUS WRITE operation. The execution cycle is directly activated by an external signal. The module is a single-width auxiliary card mounted on a rear slot adjacent to the crate ancillary card. The application of the module to the TOPAZ data acquisition system of TRISTAN is discussed, and the circuit itself is described.

miRNEST database: an integrative approach in microRNA search and annotation

PubMed Central

Szcześniak, Michał Wojciech; Deorowicz, Sebastian; Gapski, Jakub; Kaczyński, Łukasz; Makałowska, Izabela

2012-01-01

Despite accumulating data on animal and plant microRNAs and their functions, existing public miRNA resources usually collect miRNAs from a very limited number of species. A lot of microRNAs, including those from model organisms, remain undiscovered. As a result there is a continuous need to search for new microRNAs. We present miRNEST (http://mirnest.amu.edu.pl), a comprehensive database of animal, plant and virus microRNAs. The core part of the database is built from our miRNA predictions conducted on Expressed Sequence Tags of 225 animal and 202 plant species. The miRNA search was performed based on sequence similarity and as many as 10 004 miRNA candidates in 221 animal and 199 plant species were discovered. Out of them only 299 have already been deposited in miRBase. Additionally, miRNEST has been integrated with external miRNA data from literature and 13 databases, which includes miRNA sequences, small RNA sequencing data, expression, polymorphisms and targets data as well as links to external miRNA resources, whenever applicable. All this makes miRNEST a considerable miRNA resource in a sense of number of species (544) that integrates a scattered miRNA data into a uniform format with a user-friendly web interface. PMID:22135287

Coupling measurements on intelligent missiles at microwave frequencies

NASA Astrophysics Data System (ADS)

Braun, Ch.; Guidi, P.; Schmidt, H. U.

1995-03-01

This paper describes our low power microwave coupling measurements on terminally guided missiles in the frequency range between 100 and 8000 MHz. The plane wave excitation experiments have been carried out in our field coupling facility, which consists of an asymmetric triplate transmission line with maximum field levels of about 40 V/m in the working volume. As test objects we examined five (semi) autonomous guided missiles. Three of them, former experimental studies from the Diehl company (GE), are presented in this paper. The test objects were positioned in the simulator in three orthogonal orientation with respect to the external field and were not connected to a power supply (inactive condition). In order to be able to systematically analyze the interaction of the external electromagnetic fields with the avionics and its wiring, we had to divide the investigations into three independent phases, namely, external interaction with the fuselage, mode of penetration to the interior of the missile and excitation of the electrical systems and the cabling. The coupling paths depend very much on the design principles of the airframe. The main threat identified was back door coupling via those wings and fins, which are not attached galvanically to the outer surface of the hull. Because of flight guidance, these parts are fastened through slots to the bearings of the motor drives inside the missile. The dominant cable resonances sometimes can be traced back to the resonances of the wings and/or fins and the type of cabling. Another threat was coupling via the long slots required for the folding wings. These shafts penetrate the whole body and enable the external fields to couple into the interior. The peak amplitudes at the ends of the cables were found to be between 50 to 500 (micro A/(V/m)), depending on the test object.

Sequence and conformational preferences at termini of α-helices in membrane proteins: role of the helix environment.

PubMed

Shelar, Ashish; Bansal, Manju

2014-12-01

α-Helices are amongst the most common secondary structural elements seen in membrane proteins and are packed in the form of helix bundles. These α-helices encounter varying external environments (hydrophobic, hydrophilic) that may influence the sequence preferences at their N and C-termini. The role of the external environment in stabilization of the helix termini in membrane proteins is still unknown. Here we analyze α-helices in a high-resolution dataset of integral α-helical membrane proteins and establish that their sequence and conformational preferences differ from those in globular proteins. We specifically examine these preferences at the N and C-termini in helices initiating/terminating inside the membrane core as well as in linkers connecting these transmembrane helices. We find that the sequence preferences and structural motifs at capping (Ncap and Ccap) and near-helical (N' and C') positions are influenced by a combination of features including the membrane environment and the innate helix initiation and termination property of residues forming structural motifs. We also find that a large number of helix termini which do not form any particular capping motif are stabilized by formation of hydrogen bonds and hydrophobic interactions contributed from the neighboring helices in the membrane protein. We further validate the sequence preferences obtained from our analysis with data from an ultradeep sequencing study that identifies evolutionarily conserved amino acids in the rat neurotensin receptor. The results from our analysis provide insights for the secondary structure prediction, modeling and design of membrane proteins. © 2014 Wiley Periodicals, Inc.

Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes

USDA-ARS?s Scientific Manuscript database

Background: BAC-based physical maps provide for sequencing across an entire genome or selected sub-genome regions of biological interest. Using the minimum tiling path as a guide, it is possible to select specific BAC clones from prioritized genome sections such as a genetically defined QTL interv...

From Arithmetic to Algebra: Sequences and Patterns as an Introductory Lesson in Seventh Grade Mathematics

ERIC Educational Resources Information Center

Aniban, Diana Grace; Chua, Von Christopher; Garcia, Jellen; Elipane, Levi Esteban

2014-01-01

Guided by the principles of lesson study as applied to microteaching, this paper discusses the results and conclusions of a series of activities done by some graduate students of De La Salle University, Philippines, in an attempt to test the applicability of the lesson--Sequence and Patterns--to facilitate the transition of seventh graders from…

Genome Sequence of Mycobacterium hassiacum DSM 44199, a Rare Source of Heat-Stable Mycobacterial Proteins

PubMed Central

Tiago, Igor; Maranha, Ana; Mendes, Vitor; Alarico, Susana; Moynihan, Patrick J.; Clarke, Anthony J.; Macedo-Ribeiro, Sandra; Pereira, Pedro J. B.

2012-01-01

Mycobacterium hassiacum is a rapidly growing mycobacterium isolated from human urine and so far the most thermophilic among mycobacterial species. Its thermotolerance and phylogenetic relationship to M. tuberculosis render its proteins attractive tools for crystallization and structure-guided drug design. We report the draft genome sequence of M. hassiacum DSM 44199. PMID:23209251

Mississippi Curriculum Framework for Banking & Finance Technology (Program CIP: 52.0803--Banking and Related Financial Programs, Other). Postsecondary Programs.

ERIC Educational Resources Information Center

Mississippi Research and Curriculum Unit for Vocational and Technical Education, State College.

This document, which is intended for use by community and junior colleges throughout Mississippi, contains curriculum frameworks for the course sequences in the banking and finance technology program. Presented in the introduction are a program description and suggested course sequence. Section I is a curriculum guide consisting of outlines for…

in silico Whole Genome Sequencer & Analyzer (iWGS): a computational pipeline to guide the design and analysis of de novo genome sequencing studies

USDA-ARS?s Scientific Manuscript database

The availability of genomes across the tree of life is highly biased toward vertebrates, pathogens, human disease models, and organisms with relatively small and simple genomes. Recent progress in genomics has enabled the de novo decoding of the genome of virtually any organism, greatly expanding it...

Intracranial placement of a new, compliant guide catheter: technical note.

PubMed

Park, Min S; Stiefel, Michael F; Fiorella, David; Kelly, Michael; McDougall, Cameron G; Albuquerque, Felipe C

2008-09-01

We describe our initial experience with the use of a novel, compliant guide catheter designed for placement within the cranial vasculature in a series of seven patients who were treated for various intracranial pathologies. Seven patients were deemed to have either tortuous supra-aortic, intracranial, and/or extracranial vasculature or to require additional microcatheter support as the result of lesion location. The patients were treated, in part, with the 6-French Neuron delivery catheter (Penumbra, Inc., San Leandro, CA) at the authors' two institutions. The guide catheter was positioned in various distal locations within the intracranial internal carotid artery or external carotid artery. Three patients were treated for unruptured intracranial aneurysms, 2 patients for intracranial atherosclerosis, 1 patient for an arteriovenous malformation, and 1 patient for a pseudoaneurysm. All lesions were successfully treated through a microcatheter advanced in a coaxial fashion through the guide catheter. There were no complications related to the positioning of the catheter. Distal intra- or extracranial placement of a specially designed, compliant guide catheter can be performed safely and may improve access and microcatheter stability in patients with tortuous vessels or difficult-to-reach lesions.

Illustrated field guide for assessing external and internal anomalies in fish

USGS Publications Warehouse

Smith, Stephen B.; Donahue, Anne P.; Lipkin, Robin J.; Blazer, Vicki; Schmitt, Christopher J.; Goede, Ronald W.

2002-01-01

Procedures are described for processing fish for examination of external and internal anomalies and pathologies indicative of exposure to environmental contaminants and other peturbations. For the procedures described here, fish are captured (preferably by electrofishing) and held alive until processing (generally < 1 h). Fish are weighed, measured, and necropsied, and a scale sample is obtained from for age determination. Information is given for the collection and preservation of tissue samples for histopathological analysis. Photographs of most abnormalities are included along with normal conditions for easier identification of external (oral, head, eye, gill, opercula, and fin) and internal (liver, spleen, gonad, and kidney) anomalies. The report also includes recommendations for record keeping, sample labeling, and shipping records, equipment, supplies,and samples. A list of suggested equipment and supplies for field processing is included as are instructions for cleaning equipment.

Sequential addition of short DNA oligos in DNA-polymerase-based synthesis reactions

DOEpatents

Gardner, Shea N [San Leandro, CA; Mariella, Jr., Raymond P.; Christian, Allen T [Tracy, CA; Young, Jennifer A [Berkeley, CA; Clague, David S [Livermore, CA

2011-01-18

A method of fabricating a DNA molecule of user-defined sequence. The method comprises the steps of preselecting a multiplicity of DNA sequence segments that will comprise the DNA molecule of user-defined sequence, separating the DNA sequence segments temporally, and combining the multiplicity of DNA sequence segments with at least one polymerase enzyme wherein the multiplicity of DNA sequence segments join to produce the DNA molecule of user-defined sequence. Sequence segments may be of length n, where n is an even or odd integer. In one embodiment the length of desired hybridizing overlap is specified by the user and the sequences and the protocol for combining them are guided by computational (bioinformatics) predictions. In one embodiment sequence segments are combined from multiple reading frames to span the same region of a sequence, so that multiple desired hybridizations may occur with different overlap lengths. In one embodiment starting sequence fragments are of different lengths, n, n+1, n+2, etc.

Principles for Promoting the Financial Sustainability of Online Programs

ERIC Educational Resources Information Center

Meyer, Katrina A.; Bruwelheide, Janis; Poulin, Russell

2009-01-01

The project described in this article was an attempt to uncover the principles of financial sustainability for online programs and to align these with a guide to managing online programs. An initial team of experienced online educators developed draft principles, which were then reviewed by an external consultant and revised; the revised…

Maximizing Your Grant Development: A Guide for CEOs.

ERIC Educational Resources Information Center

Snyder, Thomas

1993-01-01

Since most private and public sources of external funding generally expect increased effort and accountability, Chief Executive Officers (CEOs) at two-year colleges must inform faculty and staff that if they do not expend extra effort their college will not receive significant grants. The CEO must also work with the college's professional…

TMDD & MS/ETMCC guide : standard for functional level traffic management data dictionary (TMDD) and message sets for external traffic management center communications

DOT National Transportation Integrated Search

2000-01-01

These draft standards are intended to work together to provide a high level of interoperability among regional and local traffic control centers. They provide consistent names, definitions and concepts similar to spelling and parts of speech to world...

Introduction to Social Psychology: Administrative Manual [And] Student Manual [And] Unit Study Guide.

ERIC Educational Resources Information Center

Rankin, Robert E.

This learning package is a three-semester-hour, independent-study course in social psychology designed for postsecondary, external degree students. Keyed to the commercially published textbook "Social Psychology: Explorations in Understanding" (Del Mar, CA: CRM, 1974), the package consists of an administrator manual, a student manual, and a…

A Comparison between SRSS-IE and SSiS-PSG Scores: Examining Convergent Validity

ERIC Educational Resources Information Center

Lane, Kathleen Lynne; Oakes, Wendy Peia; Common, Eric Alan; Zorigian, Kris; Brunsting, Nelson C.; Schatschneider, Christopher

2015-01-01

We report findings of a validation study comparing two screening tools: the Student Risk Screening Scale-Internalizing and Externalizing (SRSS-IE, an adapted version of the Student Risk Screening Scale) and the Social Skills Improvement System-Performance Screening Guide (SSiS-PSG). Participants included 458 kindergarten through fifth-grade…

Additional Evidence of Convergent Validity between SRSS-IE and SSiS-PSG Scores

ERIC Educational Resources Information Center

Lane, Kathleen Lynne; Oakes, Wendy Peia; Ennis, Robin Parks; Royer, David James

2015-01-01

We report findings of a validity study comparing two screening tools: the Student Risk Screening Scale-Internalizing and Externalizing (SRSS-IE) and the Social Skills Improvement System-Performance Screening Guide (SSiS-PSG; Elliott & Gresham, 2007). Participants were 1,680 kindergarten through sixth-grade elementary students from three…

Identifying Students with Mental Health Issues: A Guide for Classroom Teachers

ERIC Educational Resources Information Center

Marsh, Robbie J.

2016-01-01

Child and adolescent mental health is a growing concern in schools. Students suffering from mental health conditions struggle in the school environment if their needs are not being met. Teachers play an important role in the identification of these students. This article highlights the distinctions between externalizing and internalizing behaviors…

Social Studies: Grade 9: Asian and African Culture Studies.

ERIC Educational Resources Information Center

New York State Education Dept., Albany. Bureau of Secondary Curriculum Development.

A framework of non-western culture, specifically Asia and Africa, is provided in this 9th grade teaching guide. It is hoped that students will understand the heritage, situations, and problems of those emerging nations. Cross-cultural comparisons help students identify likenesses, differences, and effects of internal and external events on a…

Do Endogenous and Exogenous Action Control Compete for Perception?

ERIC Educational Resources Information Center

Pfister, Roland; Heinemann, Alexander; Kiesel, Andrea; Thomaschke, Roland; Janczyk, Markus

2012-01-01

Human actions are guided either by endogenous action plans or by external stimuli in the environment. These two types of action control seem to be mediated by neurophysiologically and functionally distinct systems that interfere if an endogenously planned action suddenly has to be performed in response to an exogenous stimulus. In this case, the…

Guiding Adolescents toward Responsible Sexual Decisions.

ERIC Educational Resources Information Center

Juhasz, Anne McCreary

Many teenagers will be pressured by either external or internal forces to become involved in sexual experiences. Assuming that adolescents will be faced with the question of whether or not to have intercourse, that this will be an individual decision involving internal control, and that each individual will have to make that decision, it becomes…

Estimating white trunk rot in aspen stands

Treesearch

Alan C. Jones; Michael E. Ostry

1998-01-01

Advanced decay caused by Phellinus tremulae was estimated in 295 trembling aspen on 30 plots in 2 Minnesota counties using existing inventory guides, and then measured by felling and sectioning the trees. In standing trees, decay volume was underestimated by 38% compared to measured decay volume in felled trees. The most reliable external indicator...

ICLUS Tools and Datasets (Version 1.2) and User's Manual: Arcgis Tools and Datasets for Modeling US Housing Density (External Review Draft)

EPA Science Inventory

This draft Geographic Information System (GIS) tool can be used to generate scenarios of housing-density changes and calculate impervious surface cover for the conterminous United States. A draft User’s Guide accompanies the tool. This product distributes the population project...

Observations of Representational Practices by Indian-Descent Children in a US Preschool Classroom: Connections among People, Spaces and Artifacts

ERIC Educational Resources Information Center

Braswell, Gregory S.

2015-01-01

This exploratory study examined children's experiences with producing and comprehending external representations in a preschool classroom. Data collection and analyses focused on how artifacts, spaces, adult-guided routines, and social conventions shape young children's representational development. Participants included 4- and…

An Effective Assessment Model for Implementing Change and Improving Learning

ERIC Educational Resources Information Center

Mince, Rose; Ebersole, Tara

2008-01-01

Assessment at Community College of Baltimore County (CCBC) involves asking the right questions and using data to determine what changes should be implemented to enhance student learning. Guided by a 5-stage design, CCBC's assessment program is faculty-driven, risk-free, and externally validated. Curricular and pedagogical changes have resulted in…

Interventions Promoting Educators' Use of Data: Research Insights and Gaps

ERIC Educational Resources Information Center

Marsh, Julie A.

2012-01-01

Background/Context: In recent years, states, districts, schools, and external partners have recognized the need to proactively foster the use of data to guide educational decision-making and practice. Understanding that data alone will not guarantee use, individuals at all levels have invested in interventions to support better access to,…

Using Quality Schemes in Adult and Community Learning: A Guide for Managers.

ERIC Educational Resources Information Center

Ewens, David; Watters, Kate

This document examines adult and community learning (ACL) and quality programs across England. The difficulties faced by local education agencies' ACL services in delivering quality are noted, along with ways quality improvement has been supported. Quality programs--whether internal or external, based on awards, or used as diagnostic tools--are…

Service Area Market Analysis: Focus on Industry and Occupation.

ERIC Educational Resources Information Center

Front Range Community Coll., Westminster, CO.

This report presents occupation and industry data (statewide and service area specific) for the purpose of assessing external forces in order to provide information to help guide policymaking at Front Range Community College. The report contains tables that display statewide occupational trends as published by the Colorado Department of Labor and…

Training Grant Scheme, 1969-1970; General Guide to Employers.

ERIC Educational Resources Information Center

Ceramics, Glass, and Mineral Products Industry Training Board, Harrow (England).

In its fourth grant scheme, the Ceramics, Glass, and Mineral Products Industry Training Board of Great Britain gives guidelines on grants available to its industries for training conducted between August 1, 1969 and July 31, 1970. It covers such aspects as grant conditions for external and internal training; training staff qualifications; rates…

Evidence from Visuomotor Adaptation for Two Partially Independent Visuomotor Systems

ERIC Educational Resources Information Center

Thaler, Lore; Todd, James T.

2010-01-01

Visual information can specify spatial layout with respect to the observer (egocentric) or with respect to an external frame of reference (allocentric). People can use both of these types of visual spatial information to guide their hands. The question arises if movements based on egocentric and movements based on allocentric visual information…

Guidelines for Self-Study and External Evaluation of Undergraduate Physics Programs

ERIC Educational Resources Information Center

American Association of Physics Teachers (NJ1), 2005

2005-01-01

Influenced by the project entitled "Strategic Programs for Innovations in Undergraduate Physics", this document is intended to guide a physics department in initial, or mid-stream evaluation of a program of undergraduate physics education. The original Guidelines were developed by the American Association of Physics Teachers (AAPT) in 1986. The…

Insights into freshman weight issues: An ethnographic study of how first-year college students make decisions about eating

USDA-ARS?s Scientific Manuscript database

The transition from high school to college represents a life turning point during which health behavior trajectories may be influenced. This study addresses the internal and external factors that guide students’ eating decisions as they are understood and relayed by students through ethnographic, qu...

77 FR 22234 - Notice of Intent To Request Public Comments

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-13

... consolidate future reviews of these rules with the next scheduled review of 16 CFR part 803. The Commission... schedule in the future to incorporate new rules, or to respond to external factors (such as changes in the... and 2018. Prohibitions Concerning Franchising. 681 Identity Theft [Red Flag] Rules.. 2018. 24 Guides...

An Instrumental Case Study Analysis of Anticipatory Leadership Practices in Community Colleges

ERIC Educational Resources Information Center

Johnson, Abe; Jones, Stephanie J.

2018-01-01

This qualitative instrumental case study explored the experiences and perceptions of seven community college leaders of their use of anticipatory leadership. Two research questions guided this study: (a) How do community colleges use anticipatory leadership to respond to internal and external changes? (b) How do community college leaders use…

Internal Acoustics Measurements of a Full Scale Advanced Ducted Propulsor Demonstrator

NASA Technical Reports Server (NTRS)

Santa Maria, O. L.; Soderman, P. T.; Horne, W. C.; Jones, M. G.; Bock, L. A.

1995-01-01

Acoustics measurements of a Pratt & Whitney full-scale ADP (Advanced Ducted Propulsor), an ultrahigh by-pass ratio engine, were conducted in the NASA Ames 40- by 80-Foot Wind Tunnel. This paper presents data from measurements taken from sensors on a fan exit guide vane in the ADP. Data from two sensors, one at mid-span and the other at the tip of the fan exit guide vane, are presented. At the blade passage frequency (BPF), the levels observed at the various engine and wind speeds were higher at the mid-span sensor than the tip sensor. The coherence between these internal sensors and external microphones were calculated and plotted as a function of angle (angles ranged from 5 degrees to 160 degrees) relative to the ADP longitudinal axis. At the highest engine and wind speeds, the coherence between the tip sensor and the external microphones was observed to decrease at higher multiples of the BPF. These results suggest that the rotor-stator interaction tones are stronger in the mid-span region than at the tip.

Highly Complementary Target RNAs Promote Release of Guide RNAs from Human Argonaute2

PubMed Central

De, Nabanita; Young, Lisa; Lau, Pick-Wei; Meisner, Nicole-Claudia; Morrissey, David V.; MacRae, Ian J.

2013-01-01

SUMMARY Argonaute proteins use small RNAs to guide the silencing of complementary target RNAs in many eukaryotes. Although small RNA biogenesis pathways are well studied, mechanisms for removal of guide RNAs from Argonaute are poorly understood. Here we show that the Argonaute2 (Ago2) guide RNA complex is extremely stable, with a half-life on the order of days. However, highly complementary target RNAs destabilize the complex and significantly accelerate release of the guide RNA from Ago2. This “unloading” activity can be enhanced by mismatches between the target and the guide 5′ end and attenuated by mismatches to the guide 3′ end. The introduction of 3′ mismatches leads to more potent silencing of abundant mRNAs in mammalian cells. These findings help to explain why the 3′ ends of mammalian microRNAs (miRNAs) rarely match their targets, suggest a mechanism for sequence-specific small RNA turnover, and offer insights for controlling small RNAs in mammalian cells. PMID:23664376

Rotation of intramedullary alignment rods affects distal femoral cutting plane in total knee arthroplasty.

PubMed

Maderbacher, Günther; Matussek, Jan; Keshmiri, Armin; Greimel, Felix; Baier, Clemens; Grifka, Joachim; Maderbacher, Hermann

2018-02-17

Intramedullary rods are widely used to align the distal femoral cut in total knee arthroplasty. We hypothesised that both coronal (varus/valgus) and sagittal (extension/flexion) cutting plane are affected by rotational changes of intramedullary femoral alignment guides. Distal femoral cuts using intramedullary alignment rods were simulated by means of a computer-aided engineering software in 4°, 6°, 8°, 10°, and 12° of valgus in relation to the femoral anatomical axis and 4° extension, neutral, as well as 4°, 8°, and 12° of flexion in relation to the femoral mechanical axis. This reflects the different angles between anatomical and mechanical axis in coronal and sagittal planes. To assess the influence of rotation of the alignment guide on the effective distal femoral cutting plane, all combinations were simulated with the rod gradually aligned from 40° of external to 40° of internal rotation. Rotational changes of the distal femoral alignment guides affect both the coronal and sagittal cutting planes. When alignment rods are intruded neutrally with regards to sagittal alignment, external rotation causes flexion, while internal rotation causes extension of the sagittal cutting plane. Simultaneously the coronal effect (valgus) decreases resulting in an increased varus of the cutting plane. However, when alignment rods are intruded in extension or flexion partly contradictory effects are observed. Generally the effect increases with the degree of valgus preset, rotation and flexion. As incorrect rotation of intramedullary alignment guides for distal femoral cuts causes significant cutting errors, exact rotational alignment is crucial. Coronal cutting errors in the distal femoral plane might result in overall leg malalignment, asymmetric extension gaps and subsequent sagittal cutting errors.

Fabrication and characterization of biomimetic multichanneled crosslinked-urethane-doped polyester tissue engineered nerve guides.

PubMed

Tran, Richard T; Choy, Wai Man; Cao, Hung; Qattan, Ibrahim; Chiao, Jung-Chih; Ip, Wing Yuk; Yeung, Kelvin Wai Kwok; Yang, Jian

2014-08-01

Biomimetic scaffolds that replicate the native architecture and mechanical properties of target tissues have been recently shown to be a very promising strategy to guide cellular growth and facilitate tissue regeneration. In this study, porous, soft, and elastic crosslinked urethane-doped polyester (CUPE) tissue engineered nerve guides were fabricated with multiple longitudinally oriented channels and an external non-porous sheath to mimic the native endoneurial microtubular and epineurium structure, respectively. The fabrication technique described herein is highly adaptable and allows for fine control over the resulting nerve guide architecture in terms of channel number, channel diameter, porosity, and mechanical properties. Biomimetic multichanneled CUPE guides were fabricated with various channel numbers and displayed an ultimate peak stress of 1.38 ± 0.22 MPa with a corresponding elongation at break of 122.76 ± 42.17%, which were comparable to that of native nerve tissue. The CUPE nerve guides were also evaluated in vivo for the repair of a 1 cm rat sciatic nerve defect. Although histological evaluations revealed collapse of the inner structure from CUPE TENGs, the CUPE nerve guides displayed fiber populations and densities comparable with nerve autograft controls after 8 weeks of implantation. These studies are the first report of a CUPE-based biomimetic multichanneled nerve guide and warrant future studies towards optimization of the channel geometry for use in neural tissue engineering. © 2013 Wiley Periodicals, Inc.

A plant growth-promoting symbiosis between Mycena galopus and Vaccinium corymbosum seedlings.

PubMed

Grelet, Gwen-Aëlle; Ba, Ren; Goeke, Dagmar F; Houliston, Gary J; Taylor, Andy F S; Durall, Daniel M

2017-11-01

Typically, Mycena species are viewed as saprotrophic fungi. However, numerous detections of Mycena spp. in the roots of green plants suggest that a continuum from saprotrophy to biotrophy could exist. In particular, mycenoid species have repeatedly been found in Ericaceae plant roots. Our study asked whether (1) Mycena species are commonly found in the roots of green Ericaceae plants; (2) Mycena sequences are limited to a single group/lineage within the genus; and (3) a Mycena sp. can behave as a beneficial root associate with a typical ericoid mycorrhizal plant (Vaccinium corymbosum), regardless of how much external labile carbon is available. We detected Mycena sequences in roots of all sampled Ericaceae plants. Our Mycena sequences clustered in four different groups distributed across the Mycena genus. Only one group could be assigned with confidence to a named species (M. galopus). Our Mycena sequences clustered with other Mycena sequences detected in roots of ericoid mycorrhizal plant species collected throughout Europe, America, and Australia. An isolate of M. galopus promoted growth of V. corymbosum seedlings in vitro regardless of external carbon supply in the media. Seedlings inoculated with M. galopus grew as well as those inoculated with the ericoid mycorrhizal fungus Rhizoscyphus ericae. Surprisingly, this M. galopus isolate colonized Vaccinium roots and formed distinctive peg-like structures. Our results suggest that Mycena species might operate along a saprotroph-symbiotic continuum with a range of ericoid mycorrhizal plant species. We discuss our results in terms of fungal partner recruitment by Ericaceae plants.

ATLAS, an integrated structural analysis and design system. Volume 1: ATLAS user's guide

NASA Technical Reports Server (NTRS)

Dreisbach, R. L. (Editor)

1979-01-01

Some of the many analytical capabilities provided by the ATLAS Version 4.0 System in the logical sequence are described in which model-definition data are prepared and the subsequent computer job is executed. The example data presented and the fundamental technical considerations that are highlighted can be used as guides during the problem solving process. This guide does not describe the details of the ATLAS capabilities, but provides an introduction to the new user of ATLAS to the level at which the complete array of capabilities described in the ATLAS User's Manual can be exploited fully.

Development of Light-Activated CRISPR Using Guide RNAs with Photocleavable Protectors.

PubMed

Jain, Piyush K; Ramanan, Vyas; Schepers, Arnout G; Dalvie, Nisha S; Panda, Apekshya; Fleming, Heather E; Bhatia, Sangeeta N

2016-09-26

The ability to remotely trigger CRISPR/Cas9 activity would enable new strategies to study cellular events with greater precision and complexity. In this work, we have developed a method to photocage the activity of the guide RNA called "CRISPR-plus" (CRISPR-precise light-mediated unveiling of sgRNAs). The photoactivation capability of our CRISPR-plus method is compatible with the simultaneous targeting of multiple DNA sequences and supports numerous modifications that can enable guide RNA labeling for use in imaging and mechanistic investigations. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Adaptive plasticity in speech perception: Effects of external information and internal predictions.

PubMed

Guediche, Sara; Fiez, Julie A; Holt, Lori L

2016-07-01

When listeners encounter speech under adverse listening conditions, adaptive adjustments in perception can improve comprehension over time. In some cases, these adaptive changes require the presence of external information that disambiguates the distorted speech signals, whereas in other cases mere exposure is sufficient. Both external (e.g., written feedback) and internal (e.g., prior word knowledge) sources of information can be used to generate predictions about the correct mapping of a distorted speech signal. We hypothesize that these predictions provide a basis for determining the discrepancy between the expected and actual speech signal that can be used to guide adaptive changes in perception. This study provides the first empirical investigation that manipulates external and internal factors through (a) the availability of explicit external disambiguating information via the presence or absence of postresponse orthographic information paired with a repetition of the degraded stimulus, and (b) the accuracy of internally generated predictions; an acoustic distortion is introduced either abruptly or incrementally. The results demonstrate that the impact of external information on adaptive plasticity is contingent upon whether the intelligibility of the stimuli permits accurate internally generated predictions during exposure. External information sources enhance adaptive plasticity only when input signals are severely degraded and cannot reliably access internal predictions. This is consistent with a computational framework for adaptive plasticity in which error-driven supervised learning relies on the ability to compute sensory prediction error signals from both internal and external sources of information. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Adaptive plasticity in speech perception: effects of external information and internal predictions

PubMed Central

Guediche, Sara; Fiez, Julie A.; Holt, Lori L.

2016-01-01

When listeners encounter speech under adverse listening conditions, adaptive adjustments in perception can improve comprehension over time. In some cases, these adaptive changes require the presence of external information that disambiguates the distorted speech signals, whereas in other cases mere exposure is sufficient. Both external (e.g. written feedback) and internal (e.g., prior word knowledge) sources of information can be used to generate predictions about the correct mapping of a distorted speech signal. We hypothesize that these predictions provide a basis for determining the discrepancy between the expected and actual speech signal that can be used to guide adaptive changes in perception. This study provides the first empirical investigation that manipulates external and internal factors through 1) the availability of explicit external disambiguating information via the presence or absence of post-response orthographic information paired with a repetition of the degraded stimulus, and 2) the accuracy of internally-generated predictions; an acoustic distortion is introduced either abruptly or incrementally. The results demonstrate that the impact of external information on adaptive plasticity is contingent upon whether the intelligibility of the stimuli permits accurate internally-generated predictions during exposure. External information sources enhance adaptive plasticity only when input signals are severely degraded and cannot reliably access internal predictions. This is consistent with a computational framework for adaptive plasticity in which error-driven supervised learning relies on the ability to compute sensory prediction error signals from both internal and external sources of information. PMID:26854531

Mucoceles of the sphenoid sinus.

PubMed

Weaver, R G; Gates, G A

1979-01-01

Mucoceles of the sphenoid sinuses are uncommon; 60 cases have been reported in the world literature to date. Signs and symptoms are caused by local expansion of the mucocele and include headache (the most common symptom), ocular field deficits, external ophthalmoplegia (particularly the sixth cranial nerve), and proptosis. Radiologic correlation in the form of plain films and polytomorgraphy is the most reliable guide in the diagnosis of sphenoid sinus disease. Therapy of these lesions is surgical, and drainage can be achieved via the external ethmoid or sublabial transseptal route. Three cases are presented: two had classical findings and the third was conspicuous by the presence of aseptic meningitis in the absence of local findings.

Stepwise-activable multifunctional peptide-guided prodrug micelles for cancerous cells intracellular drug release

NASA Astrophysics Data System (ADS)

Zhang, Jing; Li, Mengfei; Yuan, Zhefan; Wu, Dan; Chen, Jia-da; Feng, Jie

2016-10-01

A novel type of stepwise-activable multifunctional peptide-guided prodrug micelles (MPPM) was fabricated for cancerous cells intracellular drug release. Deca-lysine sequence (K10), a type of cell-penetrating peptide, was synthesized and terminated with azido-glycine. Then a new kind of molecule, alkyne modified doxorubicin (DOX) connecting through disulfide bond (DOX-SS-alkyne), was synthesized. After coupling via Cu-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry reaction, reduction-sensitive peptide-guided prodrug was obtained. Due to the amphiphilic property of the prodrug, it can assemble to form micelles. To prevent the nanocarriers from unspecific cellular uptake, the prodrug micelles were subsequently modified with 2,3-dimethyl maleic anhydride to obtain MPPM with a negatively charged outer shell. In vitro studies showed that MPPM could be shielded from cells under psychological environment. However, when arriving at mild acidic tumor site, the cell-penetrating capacity of MPPM would be activated by charge reversal of the micelles via hydrolysis of acid-labile β-carboxylic amides and regeneration of K10, which enabled efficient internalization of MPPM by tumor cells as well as following glutathione- and protease-induced drug release inside the cancerous cells. Furthermore, since the guide peptide sequences can be accurately designed and synthesized, it can be easily changed for various functions, such as targeting peptide, apoptotic peptide, even aptamers, only need to be terminated with azido-glycine. This method can be used as a template for reduction-sensitive peptide-guided prodrug for cancer therapy.

Gain-guided soliton fiber laser with high-quality rectangle spectrum for ultrafast time-stretch microscopy.

PubMed

Hu, Song; Yao, Jian; Liu, Meng; Luo, Ai-Ping; Luo, Zhi-Chao; Xu, Wen-Cheng

2016-05-16

The ultrafast time-stretch microscopy has been proposed to enhance the temporal resolution of a microscopy system. The optical source is a key component for ultrafast time-stretch microscopy system. Herein, we reported on the gain-guided soliton fiber laser with high-quality rectangle spectrum for ultrafast time-stretch microscopy. By virtue of the excellent characteristics of the gain-guided soliton, the output power and the 3-dB bandwidth of the stable mode-locked soliton could be up to 3 mW and 33.7 nm with a high-quality rectangle shape, respectively. With the proposed robust optical source, the ultrafast time-stretch microscopy with the 49.6 μm resolution and a scan rate of 11 MHz was achieved without the external optical amplification. The obtained results demonstrated that the gain-guided soliton fiber laser could be used as an alternative high-quality optical source for ultrafast time-stretch microscopy and will introduce some applications in fields such as biology, chemical, and optical sensing.

Direct and Inverse Techniques of Guided-Mode Resonance Filters Designs

NASA Technical Reports Server (NTRS)

Tibuleac, Sorin; Magnusson, Robert; Maldonado, Theresa A.; Zuffada, Cinzia

1997-01-01

Guided-mode resonances arise in single or multilayer waveguides where one or more homogeneous layers are replaced by diffraction gratings (Fig. 1.) The diffractive element enables an electromagnetic wave incident on a waveguide grating to be coupled to the waveguide modes supportable by the structure in the absence of the modulation (i.e. the difference between the high and low dielectric constants of the grating) at specific values of the wavelength and incident angle. The periodic modulation of the guide makes the structure leaky, preventing sustained propagation of modes in the waveguide and coupling the waves out into the substrate and cover. As the wavelength is varied around resonance a rapid variation in the intensities of the external propagating waves occurs. By selecting a grating period small enough to eliminate the higher-order propagating waves, an increase in the zero-order intensities up to 100% can result. The pronounced frequency selectivity of guided-mode resonances in dielectric waveguide gratings can be applied to design high-efficiency reflection and transmission filters [1-3].

Generic precise augmented reality guiding system and its calibration method based on 3D virtual model.

PubMed

Liu, Miao; Yang, Shourui; Wang, Zhangying; Huang, Shujun; Liu, Yue; Niu, Zhenqi; Zhang, Xiaoxuan; Zhu, Jigui; Zhang, Zonghua

2016-05-30

Augmented reality system can be applied to provide precise guidance for various kinds of manual works. The adaptability and guiding accuracy of such systems are decided by the computational model and the corresponding calibration method. In this paper, a novel type of augmented reality guiding system and the corresponding designing scheme are proposed. Guided by external positioning equipment, the proposed system can achieve high relative indication accuracy in a large working space. Meanwhile, the proposed system is realized with a digital projector and the general back projection model is derived with geometry relationship between digitized 3D model and the projector in free space. The corresponding calibration method is also designed for the proposed system to obtain the parameters of projector. To validate the proposed back projection model, the coordinate data collected by a 3D positioning equipment is used to calculate and optimize the extrinsic parameters. The final projecting indication accuracy of the system is verified with subpixel pattern projecting technique.

[Efficient genome editing in human pluripotent stem cells through CRISPR/Cas9].

PubMed

Liu, Gai-gai; Li, Shuang; Wei, Yu-da; Zhang, Yong-xian; Ding, Qiu-rong

2015-11-01

The RNA-guided CRISPR (clustered regularly interspaced short palindromic repeat)-associated Cas9 nuclease has offered a new platform for genome editing with high efficiency. Here, we report the use of CRISPR/Cas9 technology to target a specific genomic region in human pluripotent stem cells. We show that CRISPR/Cas9 can be used to disrupt a gene by introducing frameshift mutations to gene coding region; to knock in specific sequences (e.g. FLAG tag DNA sequence) to targeted genomic locus via homology directed repair; to induce large genomic deletion through dual-guide multiplex. Our results demonstrate the versatile application of CRISPR/Cas9 in stem cell genome editing, which can be widely utilized for functional studies of genes or genome loci in human pluripotent stem cells.

Looking beyond the exome: a phenotype-first approach to molecular diagnostic resolution in rare and undiagnosed diseases.

PubMed

Pena, Loren D M; Jiang, Yong-Hui; Schoch, Kelly; Spillmann, Rebecca C; Walley, Nicole; Stong, Nicholas; Rapisardo Horn, Sarah; Sullivan, Jennifer A; McConkie-Rosell, Allyn; Kansagra, Sujay; Smith, Edward C; El-Dairi, Mays; Bellet, Jane; Keels, Martha Ann; Jasien, Joan; Kranz, Peter G; Noel, Richard; Nagaraj, Shashi K; Lark, Robert K; Wechsler, Daniel S G; Del Gaudio, Daniela; Leung, Marco L; Hendon, Laura G; Parker, Collette C; Jones, Kelly L; Goldstein, David B; Shashi, Vandana

2018-04-01

PurposeTo describe examples of missed pathogenic variants on whole-exome sequencing (WES) and the importance of deep phenotyping for further diagnostic testing.MethodsGuided by phenotypic information, three children with negative WES underwent targeted single-gene testing.ResultsIndividual 1 had a clinical diagnosis consistent with infantile systemic hyalinosis, although WES and a next-generation sequencing (NGS)-based ANTXR2 test were negative. Sanger sequencing of ANTXR2 revealed a homozygous single base pair insertion, previously missed by the WES variant caller software. Individual 2 had neurodevelopmental regression and cerebellar atrophy, with no diagnosis on WES. New clinical findings prompted Sanger sequencing and copy number testing of PLA2G6. A novel homozygous deletion of the noncoding exon 1 (not included in the WES capture kit) was detected, with extension into the promoter, confirming the clinical suspicion of infantile neuroaxonal dystrophy. Individual 3 had progressive ataxia, spasticity, and magnetic resonance image changes of vanishing white matter leukoencephalopathy. An NGS leukodystrophy gene panel and WES showed a heterozygous pathogenic variant in EIF2B5; no deletions/duplications were detected. Sanger sequencing of EIF2B5 showed a frameshift indel, probably missed owing to failure of alignment.ConclusionThese cases illustrate potential pitfalls of WES/NGS testing and the importance of phenotype-guided molecular testing in yielding diagnoses.

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences.

PubMed

Mirarab, Siavash; Nguyen, Nam; Guo, Sheng; Wang, Li-San; Kim, Junhyong; Warnow, Tandy

2015-05-01

We introduce PASTA, a new multiple sequence alignment algorithm. PASTA uses a new technique to produce an alignment given a guide tree that enables it to be both highly scalable and very accurate. We present a study on biological and simulated data with up to 200,000 sequences, showing that PASTA produces highly accurate alignments, improving on the accuracy and scalability of the leading alignment methods (including SATé). We also show that trees estimated on PASTA alignments are highly accurate--slightly better than SATé trees, but with substantial improvements relative to other methods. Finally, PASTA is faster than SATé, highly parallelizable, and requires relatively little memory.

Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a.

PubMed

Swarts, Daan C; van der Oost, John; Jinek, Martin

2017-04-20

The CRISPR-associated protein Cas12a (Cpf1), which has been repurposed for genome editing, possesses two distinct nuclease activities: endoribonuclease activity for processing its own guide RNAs and RNA-guided DNase activity for target DNA cleavage. To elucidate the molecular basis of both activities, we determined crystal structures of Francisella novicida Cas12a bound to guide RNA and in complex with an R-loop formed by a non-cleavable guide RNA precursor and a full-length target DNA. Corroborated by biochemical experiments, these structures reveal the mechanisms of guide RNA processing and pre-ordering of the seed sequence in the guide RNA that primes Cas12a for target DNA binding. Furthermore, the R-loop complex structure reveals the strand displacement mechanism that facilitates guide-target hybridization and suggests a mechanism for double-stranded DNA cleavage involving a single active site. Together, these insights advance our mechanistic understanding of Cas12a enzymes and may contribute to further development of genome editing technologies. Copyright © 2017 Elsevier Inc. All rights reserved.

Plasma arc welding weld imaging

NASA Technical Reports Server (NTRS)

Rybicki, Daniel J. (Inventor); Mcgee, William F. (Inventor)

1994-01-01

A welding torch for plasma arc welding apparatus has a transparent shield cup disposed about the constricting nozzle, the cup including a small outwardly extending polished lip. A guide tube extends externally of the torch and has a free end adjacent to the lip. First and second optical fiber bundle assemblies are supported within the guide tube. Light from a strobe light is transmitted along one of the assemblies to the free end and through the lip onto the weld site. A lens is positioned in the guide tube adjacent to the second assembly and focuses images of the weld site onto the end of the fiber bundle of the second assembly and these images are transmitted along the second assembly to a video camera so that the weld site may be viewed continuously for monitoring the welding process.

An Outbreak of Streptococcus pyogenes in a Mental Health Facility: Advantage of Well-Timed Whole-Genome Sequencing Over emm Typing.

PubMed

Bergin, Sarah M; Periaswamy, Balamurugan; Barkham, Timothy; Chua, Hong Choon; Mok, Yee Ming; Fung, Daniel Shuen Sheng; Su, Alex Hsin Chuan; Lee, Yen Ling; Chua, Ming Lai Ivan; Ng, Poh Yong; Soon, Wei Jia Wendy; Chu, Collins Wenhan; Tan, Siyun Lucinda; Meehan, Mary; Ang, Brenda Sze Peng; Leo, Yee Sin; Holden, Matthew T G; De, Partha; Hsu, Li Yang; Chen, Swaine L; de Sessions, Paola Florez; Marimuthu, Kalisvar

2018-05-09

OBJECTIVEWe report the utility of whole-genome sequencing (WGS) conducted in a clinically relevant time frame (ie, sufficient for guiding management decision), in managing a Streptococcus pyogenes outbreak, and present a comparison of its performance with emm typing.SETTINGA 2,000-bed tertiary-care psychiatric hospital.METHODSActive surveillance was conducted to identify new cases of S. pyogenes. WGS guided targeted epidemiological investigations, and infection control measures were implemented. Single-nucleotide polymorphism (SNP)-based genome phylogeny, emm typing, and multilocus sequence typing (MLST) were performed. We compared the ability of WGS and emm typing to correctly identify person-to-person transmission and to guide the management of the outbreak.RESULTSThe study included 204 patients and 152 staff. We identified 35 patients and 2 staff members with S. pyogenes. WGS revealed polyclonal S. pyogenes infections with 3 genetically distinct phylogenetic clusters (C1-C3). Cluster C1 isolates were all emm type 4, sequence type 915 and had pairwise SNP differences of 0-5, which suggested recent person-to-person transmissions. Epidemiological investigation revealed that cluster C1 was mediated by dermal colonization and transmission of S. pyogenes in a male residential ward. Clusters C2 and C3 were genomically diverse, with pairwise SNP differences of 21-45 and 26-58, and emm 11 and mostly emm120, respectively. Clusters C2 and C3, which may have been considered person-to-person transmissions by emm typing, were shown by WGS to be unlikely by integrating pairwise SNP differences with epidemiology.CONCLUSIONSWGS had higher resolution than emm typing in identifying clusters with recent and ongoing person-to-person transmissions, which allowed implementation of targeted intervention to control the outbreak.Infect Control Hosp Epidemiol 2018;1-9.

Examination of CRISPR/Cas9 design tools and the effect of target site accessibility on Cas9 activity.

PubMed

Lee, Ciaran M; Davis, Timothy H; Bao, Gang

2018-04-01

What is the topic of this review? In this review, we analyse the performance of recently described tools for CRISPR/Cas9 guide RNA design, in particular, design tools that predict CRISPR/Cas9 activity. What advances does it highlight? Recently, many tools designed to predict CRISPR/Cas9 activity have been reported. However, the majority of these tools lack experimental validation. Our analyses indicate that these tools have poor predictive power. Our preliminary results suggest that target site accessibility should be considered in order to develop better guide RNA design tools with improved predictive power. The recent adaptation of the clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system for targeted genome engineering has led to its widespread application in many fields worldwide. In order to gain a better understanding of the design rules of CRISPR/Cas9 systems, several groups have carried out large library-based screens leading to some insight into sequence preferences among highly active target sites. To facilitate CRISPR/Cas9 design, these studies have spawned a plethora of guide RNA (gRNA) design tools with algorithms based solely on direct or indirect sequence features. Here, we demonstrate that the predictive power of these tools is poor, suggesting that sequence features alone cannot accurately inform the cutting efficiency of a particular CRISPR/Cas9 gRNA design. Furthermore, we demonstrate that DNA target site accessibility influences the activity of CRISPR/Cas9. With further optimization, we hypothesize that it will be possible to increase the predictive power of gRNA design tools by including both sequence and target site accessibility metrics. © 2017 The Authors. Experimental Physiology © 2017 The Physiological Society.

Whole genome analysis of CRISPR Cas9 sgRNA off-target homologies via an efficient computational algorithm.

PubMed

Zhou, Hong; Zhou, Michael; Li, Daisy; Manthey, Joseph; Lioutikova, Ekaterina; Wang, Hong; Zeng, Xiao

2017-11-17

The beauty and power of the genome editing mechanism, CRISPR Cas9 endonuclease system, lies in the fact that it is RNA-programmable such that Cas9 can be guided to any genomic loci complementary to a 20-nt RNA, single guide RNA (sgRNA), to cleave double stranded DNA, allowing the introduction of wanted mutations. Unfortunately, it has been reported repeatedly that the sgRNA can also guide Cas9 to off-target sites where the DNA sequence is homologous to sgRNA. Using human genome and Streptococcus pyogenes Cas9 (SpCas9) as an example, this article mathematically analyzed the probabilities of off-target homologies of sgRNAs and discovered that for large genome size such as human genome, potential off-target homologies are inevitable for sgRNA selection. A highly efficient computationl algorithm was developed for whole genome sgRNA design and off-target homology searches. By means of a dynamically constructed sequence-indexed database and a simplified sequence alignment method, this algorithm achieves very high efficiency while guaranteeing the identification of all existing potential off-target homologies. Via this algorithm, 1,876,775 sgRNAs were designed for the 19,153 human mRNA genes and only two sgRNAs were found to be free of off-target homology. By means of the novel and efficient sgRNA homology search algorithm introduced in this article, genome wide sgRNA design and off-target analysis were conducted and the results confirmed the mathematical analysis that for a sgRNA sequence, it is almost impossible to escape potential off-target homologies. Future innovations on the CRISPR Cas9 gene editing technology need to focus on how to eliminate the Cas9 off-target activity.

RNA-Catalyzed RNA Ligation on an External RNA Template

NASA Technical Reports Server (NTRS)

McGinness, Kathleen E.; Joyce, Gerald F.

2002-01-01

Variants of the hc ligase ribozyme, which catalyzes ligation of the 3' end of an RNA substrate to the 5' end of the ribozyme, were utilized to evolve a ribozyme that catalyzes ligation reactions on an external RNA template. The evolved ribozyme catalyzes the joining of an oligonucleotide 3'-hydroxyl to the 5'-triphosphate of an RNA hairpin molecule. The ribozyme can also utilize various substrate sequences, demonstrating a largely sequence-independent mechanism for substrate recognition. The ribozyme also carries out the ligation of two oligonucleotides that are bound at adjacent positions on a complementary template. Finally, it catalyzes addition of mononucleoside '5-triphosphates onto the '3 end of an oligonucleotide primer in a template-dependent manner. The development of ribozymes that catalyze polymerase-type reactions contributes to the notion that an RNA world could have existed during the early history of life on Earth.

Perinatal and paediatric post-mortem magnetic resonance imaging (PMMR): sequences and technique

PubMed Central

Norman, Wendy; Jawad, Noorulhuda; Jones, Rod; Taylor, Andrew M

2016-01-01

As post-mortem MRI (PMMR) becomes more widely used for investigation following perinatal and paediatric deaths, the best possible images should be acquired. In this article, we review the most widely used published PMMR sequences, together with outlining our acquisition protocol and sequence parameters for foetal, perinatal and paediatric PMMR. We give examples of both normal and abnormal appearances, so that the reader can understand the logic behind each acquisition step before interpretation, as a useful day-to-day reference guide to performing PMMR. PMID:26916282

Effect of Structured Touch and Guided Imagery for Pain and Anxiety in Elective Joint Replacement Patients--A Randomized Controlled Trial: M-TIJRP.

PubMed

Forward, John Brent; Greuter, Nancy Elizabeth; Crisall, Santa J; Lester, Houston F

2015-01-01

Postoperative management of pain after total joint arthroplasty remains a challenge despite advancements in analgesics. Evidence shows that complementary modalities with mind-body and tactile-based approaches are valid and effective adjuncts to reduce pain and anxiety postoperatively. To investigate the effectiveness of the "M" Technique (M), a registered method of structured touch using a set sequence and number of strokes, and a consistent level of pressure on hands and feet, compared with guided imagery and usual care, for the reduction of pain and anxiety in patients undergoing elective total knee or hip replacement surgery. Randomized controlled trial: M-TIJRP (MiTechnique and guided Imagery in Joint Replacement Patients [Mighty Junior P]). At a community hospital, 225 male and female patients, aged 38 to 90 years, undergoing elective total hip or knee replacement were randomly assigned to 1 of 3 groups (75 patients in each): M, guided imagery, or usual care. They were blinded to their assignment until the intervention. Reduction of pain and anxiety postoperatively. Secondary outcomes measured use of pain medication and patient satisfaction. This study yielded positive findings for the management of pain and anxiety in patients undergoing elective joint replacement using M and guided imagery for 18 to 20 minutes compared with usual care. M showed the largest predicted decreases in both pain and anxiety between groups. There was no significant difference in narcotic pain medication use between groups. Patient satisfaction survey ratings were highest for M, followed by guided imagery. The benefit of M may be because of the specifically structured sequence of touch by competent caring, trained providers.

Effect of Structured Touch and Guided Imagery for Pain and Anxiety in Elective Joint Replacement Patients—A Randomized Controlled Trial: M-TIJRP

PubMed Central

Forward, John Brent; Greuter, Nancy Elizabeth; Crisall, Santa J; Lester, Houston F

2015-01-01

Context: Postoperative management of pain after total joint arthroplasty remains a challenge despite advancements in analgesics. Evidence shows that complementary modalities with mind-body and tactile-based approaches are valid and effective adjuncts to reduce pain and anxiety postoperatively. Objective: To investigate the effectiveness of the “M” Technique (M), a registered method of structured touch using a set sequence and number of strokes, and a consistent level of pressure on hands and feet, compared with guided imagery and usual care, for the reduction of pain and anxiety in patients undergoing elective total knee or hip replacement surgery. Methods: Randomized controlled trial: M-TIJRP (MiTechnique and guided Imagery in Joint Replacement Patients [Mighty Junior P]). At a community hospital, 225 male and female patients, aged 38 to 90 years, undergoing elective total hip or knee replacement were randomly assigned to 1 of 3 groups (75 patients in each): M, guided imagery, or usual care. They were blinded to their assignment until the intervention. Main Outcome Measures: Reduction of pain and anxiety postoperatively. Secondary outcomes measured use of pain medication and patient satisfaction. Results: This study yielded positive findings for the management of pain and anxiety in patients undergoing elective joint replacement using M and guided imagery for 18 to 20 minutes compared with usual care. M showed the largest predicted decreases in both pain and anxiety between groups. There was no significant difference in narcotic pain medication use between groups. Patient satisfaction survey ratings were highest for M, followed by guided imagery. Conclusion: The benefit of M may be because of the specifically structured sequence of touch by competent caring, trained providers. PMID:26222093

Perceived Barriers by University Students in the Practice of Physical Activities

PubMed Central

Gómez-López, Manuel; Gallegos, Antonio Granero; Extremera, Antonio Baena

2010-01-01

The main goal of this research is to study in detail the main characteristics of university students in order to find out the reasons why they have adopted an inactive lifestyle. In order to do so, a questionnaire on the analysis of sports habits and lifestyle was given to 323 students. They were taken from a representative sample of 1834 students. These 323 students had pointed out at the moment of the fieldwork, not having practiced any sport in their spare time. Our findings point out that there are diverse reasons for this. On one hand, reasons referred to as external barriers such as lack of time, on the other hand, internal barriers such as not liking the physical activity, not seeing its practicality or usefulness, feeling lazy or with apathy, or thinking that they are not competent in this type of activities. Other reasons such as the lack of social support are grouped within the external barriers. Finally, it is important to stress that there are also differences based on gender with respect to motivation. Key points External barriers prevail in university students. The lack of time is among the most highlighted ones. Statistically significant results have been found regarding the gender variable. The results are very important since they are considered to be valuable information for university institutions when guiding and diversifying their offer of physical and sport activities. Also as a guide in the design of support policies and national sport management guidelines. PMID:24149629