Molecular and phenotypic characterization of Listeria monocytogenes from U.S. Department of Agriculture Food Safety and Inspection Service surveillance of ready-to-eat foods and processing facilities.

PubMed

Ward, Todd J; Evans, Peter; Wiedmann, Martin; Usgaard, Thomas; Roof, Sherry E; Stroika, Steven G; Hise, Kelley

2010-05-01

A panel of 501 Listeria monocytogenes isolates obtained from the U.S. Department of Agriculture Food Safety and Inspection Service monitoring programs for ready-to-eat (RTE) foods were subtyped by multilocus genotyping (MLGT) and by sequencing the virulence gene inlA, which codes for internalin. MLGT analyses confirmed that clonal lineages associated with previous epidemic outbreaks were rare (7.6%) contaminants of RTE meat and poultry products and their production environments. Conversely, sequence analyses revealed mutations leading to 11 different premature stop codons (PMSCs) in inlA, including three novel PMSC mutations, and revealed that the frequency of these virulence-attenuating mutations among RTE isolates (48.5%) was substantially higher than previously appreciated. Significant differences (P < 0.001) in the frequency of inlA PMSCs were observed between lineages and between major serogroups, which could partially explain differences in association of these subtypes with human listeriosis. Interrogation of single-nucleotide polymorphisms responsible for PMSCs in inlA improved strain resolution among isolates with the 10 most common pulsed-field gel electrophoresis (PFGE) patterns, 8 of which included isolates with a PMSC in inlA. The presence or absence of PMSCs in inlA accounted for significant differences (P < 0.05) in Caco-2 invasion efficiencies among isolates with identical PFGE patterns, and the proportion of PulseNet entries from clinical sources was significantly higher (P < 0.001) for PFGE patterns exclusively from isolates with full-length inlA. These results indicated that integration of PFGE and DNA sequence-based subtyping provides an improved framework for prediction of relative risk associated with L. monocytogenes strains from RTE foods.

Prevalence, Molecular Characterization, and Antibiotic Susceptibility of Vibrio parahaemolyticus from Ready-to-Eat Foods in China

PubMed Central

Xie, Tengfei; Xu, Xiaoke; Wu, Qingping; Zhang, Jumei; Cheng, Jianheng

2016-01-01

Vibrio parahaemolyticus is the leading cause of foodborne outbreaks, particularly outbreaks associated with consumption of fish and shellfish, and represents a major threat to human health worldwide. This bacterium harbors two main virulence factors: the thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH). Additionally, various serotypes have been identified. The extensive use of antibiotics is a contributing factor to the increasing incidence of antimicrobial-resistant V. parahaemolyticus. In the current study, we aimed to determine the incidence and features of V. parahaemolyticus in ready-to-eat (RTE) foods in China. We found 39 V. parahaemolyticus strains on Chinese RTE foods through investigation of 511 RTE foods samples from 24 cities in China. All isolates were analyzed for the presence of tdh and trh gene by PCR, serotyping was performed using multiplex PCR, antibiotic susceptibility analysis was carried out using the disk diffusion method, and molecular typing was performed using enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) typing and multilocus sequence typing (MLST). The results showed that none of the isolates were positive for tdh and trh. Most of the isolates (33.3%) were serotype O2. Antimicrobial susceptibility results indicated that most strains were resistant to streptomycin (89.7%), cefazolin (51.3%), and ampicillin (51.3%). The isolates were grouped into five clusters by ERIC-PCR and four clusters by MLST. We updated 10 novel loci and 33 sequence types (STs) in the MLST database. Thus, our findings demonstrated the presence of V. parahaemolyticus in Chinese RTE foods, provided insights into the dissemination of antibiotic-resistant strains, and improved our knowledge of methods of microbiological risk assessment in RTE foods. PMID:27148231

When practice precedes theory - A mixed methods evaluation of students' learning experiences in an undergraduate study program in nursing.

PubMed

Falk, Kristin; Falk, Hanna; Jakobsson Ung, Eva

2016-01-01

A key area for consideration is determining how optimal conditions for learning can be created. Higher education in nursing aims to prepare students to develop their capabilities to become independent professionals. The aim of this study was to evaluate the effects of sequencing clinical practice prior to theoretical studies on student's experiences of self-directed learning readiness and students' approach to learning in the second year of a three-year undergraduate study program in nursing. 123 nursing students was included in the study and divided in two groups. In group A (n = 60) clinical practice preceded theoretical studies. In group (n = 63) theoretical studies preceded clinical practice. Learning readiness was measured using the Directed Learning Readiness Scale for Nursing Education (SDLRSNE), and learning process was measured using the revised two-factor version of the Study Process Questionnaire (R-SPQ-2F). Students were also asked to write down their personal reflections throughout the course. By using a mixed method design, the qualitative component focused on the students' personal experiences in relation to the sequencing of theoretical studies and clinical practice. The quantitative component provided information about learning readiness before and after the intervention. Our findings confirm that students are sensitive and adaptable to their learning contexts, and that the sequencing of courses is subordinate to a pedagogical style enhancing students' deep learning approaches, which needs to be incorporated in the development of undergraduate nursing programs. Copyright © 2015 Elsevier Ltd. All rights reserved.

Unpacking the Black Box of the Chicago School Readiness Project Intervention: The Mediating Roles of Teacher-Child Relationship Quality and Self-Regulation

ERIC Educational Resources Information Center

Jones, Stephanie M.; Bub, Kristen L.; Raver, C. Cybele

2013-01-01

Research Findings: This study examines the theory of change of the Chicago School Readiness Project (CSRP), testing a sequence of theory-derived mediating mechanisms that include the quality of teacher-child relationships and children's self-regulation. The CSRP is a multicomponent teacher and classroom-focused intervention, and its…

Derivatized versions of ligase enzymes for constructing DNA sequences

DOEpatents

Mariella, Jr., Raymond P.; Christian, Allen T [Tracy, CA; Tucker, James D [Novi, MN; Dzenitis, John M [Livermore, CA; Papavasiliou, Alexandros P [Oakland, CA

2006-08-15

A method of making very long, double-stranded synthetic poly-nucleotides. A multiplicity of short oligonucleotides is provided. The short oligonucleotides are sequentially hybridized to each other. Enzymatic ligation of the oligonucleotides provides a contiguous piece of PCR-ready DNA of predetermined sequence.

Wet countdown demonstration and flight readiness firing

NASA Technical Reports Server (NTRS)

1981-01-01

The prelaunch tests for the Space Transportation System 1 flight are briefly described. Testing is divided into two major sections: the wet countdown demonstration test/flight readiness firing, which includes a 20 second test firing of the orbiter's three main engines, and a mission verification test, which is centered on flight and landing operations. The functions of the countdown sequence are listed and end of mission and mission abort exercises are described.

Apollo experience report the command and service module milestone review process

NASA Technical Reports Server (NTRS)

Brendle, H. L.; York, J. A.

1974-01-01

The sequence of the command and service module milestone review process is given, and the Customer Acceptance Readiness Review and Flight Readiness Review plans are presented. Contents of the System Summary Acceptance Documents for the two formal spacecraft reviews are detailed, and supplemental data required for presentation to the review boards are listed. Typical forms, correspondence, supporting documentation, and minutes of a board meeting are included.

Lights, camera, action: high-throughput plant phenotyping is ready for a close-up

USDA-ARS?s Scientific Manuscript database

Modern techniques for crop improvement rely on both DNA sequencing and accurate quantification of plant traits to identify genes and germplasm of interest. With rapid advances in DNA sequencing technologies, plant phenotyping is now a bottleneck in advancing crop yields [1,2]. Furthermore, the envir...

NPOESS Preparatory Project (NPP) Science Overview

NASA Technical Reports Server (NTRS)

Butler, James J.

2011-01-01

NPP Instruments are: (1) well understood thanks to instrument comprehensive test, characterization and calibration programs. (2) Government team ready for October 25 launch followed by instrument activation and Intensive Calibration/Validation (ICV). NPP Data Products preliminary work includes: (1) JPSS Center for Satellite Applications and Research (STAR) team ready to support NPP ICV and operational data products. (2) NASA NPP science team ready to support NPP ICV and EOS data continuity.

Isolation, molecular and phenotypic characterization of Cronobacter spp. in ready-to-eat salads and foods from Japanese cuisine commercialized in Brazil.

PubMed

Vasconcellos, Luiza; Carvalho, Carla Trece; Tavares, Rodrigo Overas; de Mello Medeiros, Valéria; de Oliveira Rosas, Carla; Silva, Júlia Nunes; Dos Reis Lopes, Silvia Maria; Forsythe, Stephen James; Brandão, Marcelo Luiz Lima

2018-05-01

The aim of this study was to detect Cronobacter from 30 samples of ready-to-eat (RTE) salads and 30 foods from Japanese cuisine as commercially available in Brazil. The detection of Cronobacter was as according to the ISO standard 22964:2017. The isolates were phenotypically characterized by Vitek 2.0 and the antibiotic susceptibility profile was determined using the standardized agar disc diffusion method. Molecular characterization was accomplished by real-time PCR targeting dnaG gene, multiplex-PCR targeting cgcA gene, and fusA allele sequencing. Twenty-seven samples (45.0%) contained Cronobacter, 14 (23.3%) samples of foods from Japanese cuisine and 13 (21.7%) samples of RTE salads. Twenty-nine unique Cronobacter isolates were selected from the 27 positive samples and were identified as C. sakazakii (n = 18), C. malonaticus (n = 8), and C. dublinensis (n = 3). A high genetic diversity was observed, with 29 Cronobacter strains being assigned to 11 different fusA alleles, a ratio of 2.6 strains by fusA allele was found. The cgcA multiplex-PCR failed to identify many of the Cronobacter isolates at the species level. Four (13.8%) Cronobacter isolates were resistant to one or more antibiotics tested (n = 12). The presence of Cronobacter in RTE foods could be a potential threat to human health and highlights the need for high levels of hygiene, particularly when preparing food for elderly, immunosuppressed persons or adults with prior underlying pathology. Epidemiological surveillance agencies should be aware of the risk that these RTE foods may represent, for these groups. Copyright © 2018 Elsevier Ltd. All rights reserved.

Antismoking Threat and Efficacy Appeals: Effects on Smoking Cessation Intentions for Smokers with Low and High Readiness to Quit

PubMed Central

Wong, Norman C. H.; Cappella, Joseph N.

2009-01-01

This study examined the effects of sequencing different types of antismoking threat and efficacy appeals on smoking cessation intentions for smokers with low and high levels of readiness to quit. An experiment was done to test predictions based on Witte's (1992) Extended Parallel Process Model and research by Cho and Salmon (2006). A national probability sample of 555 adult smokers was recruited to take part in this study. Results found a positive two-way interaction effect between message threat and perceived level of message efficacy on intentions to seek help for quitting. A three-way interaction effect was found between message threat, perceived level of message efficacy, and readiness to quit on quitting intentions. Both threat and efficacy were important for smokers with low readiness to quit, whereas efficacy was most important among smokers with high readiness to quit. Implications of the results for antismoking campaigns are discussed along with limitations and future directions. PMID:20046966

Bimodal imprint chips for peptide screening: integration of high-throughput sequencing by MS and affinity analyses by surface plasmon resonance imaging.

PubMed

Wang, Weizhi; Li, Menglin; Wei, Zewen; Wang, Zihua; Bu, Xiangli; Lai, Wenjia; Yang, Shu; Gong, He; Zheng, Hui; Wang, Yuqiao; Liu, Ying; Li, Qin; Fang, Qiaojun; Hu, Zhiyuan

2014-04-15

Peptide probes and drugs have widespread applications in disease diagnostics and therapy. The demand for peptides ligands with high affinity and high specificity toward various targets has surged in the biomedical field in recent years. The traditional peptide screening procedure involves selection, sequencing, and characterization steps, and each step is manual and tedious. Herein, we developed a bimodal imprint microarray system to embrace the whole peptide screening process. Silver-sputtered silicon chip fabricated with microwell array can trap and pattern the candidate peptide beads in a one-well-one-bead manner. Peptides on beads were photocleaved in situ. A portion of the peptide in each well was transferred to a gold-coated chip to print the peptide array for high-throughput affinity analyses by surface plasmon resonance imaging (SPRi), and the peptide left in the silver-sputtered chip was ready for in situ single bead sequencing by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Using the bimodal imprint chip system, affinity peptides toward AHA were efficiently screened out from the 7 × 10(4) peptide library. The method provides a solution for high efficiency peptide screening.

Characterisation and Next-generation Sequencing Analysis of Unknown Arboviruses

DTIC Science & Technology

2012-09-01

on the development of real- time PCR detection assays for Vibrio cholerae, a water-borne bacterium responsible for severe enteric disease. From...specific sequence [22]. The length of time from harvesting virus to generating samples that are ready for sequencing takes about two weeks, which is a...two viruses, and on day 4 post infection significant and widespread cytopathic effect was observed. The viruses were harvested by ultracentrifugation

Recursive sequences in first-year calculus

NASA Astrophysics Data System (ADS)

Krainer, Thomas

2016-02-01

This article provides ready-to-use supplementary material on recursive sequences for a second-semester calculus class. It equips first-year calculus students with a basic methodical procedure based on which they can conduct a rigorous convergence or divergence analysis of many simple recursive sequences on their own without the need to invoke inductive arguments as is typically required in calculus textbooks. The sequences that are accessible to this kind of analysis are predominantly (eventually) monotonic, but also certain recursive sequences that alternate around their limit point as they converge can be considered.

Event-specific real-time detection and quantification of genetically modified Roundup Ready soybean.

PubMed

Huang, Chia-Chia; Pan, Tzu-Ming

2005-05-18

The event-specific real-time detection and quantification of Roundup Ready soybean (RRS) using an ABI PRISM 7700 sequence detection system with light upon extension (LUX) primer was developed in this study. The event-specific primers were designed, targeting the junction of the RRS 5' integration site and the endogenous gene lectin1. Then, a standard reference plasmid was constructed that carried both of the targeted sequences for quantitative analysis. The detection limit of the LUX real-time PCR system was 0.05 ng of 100% RRS genomic DNA, which was equal to 20.5 copies. The range of quantification was from 0.1 to 100%. The sensitivity and range of quantification successfully met the requirement of the labeling rules in the European Union and Taiwan.

Ready or Not: The Academic College Readiness of Southeast Asian Americans

ERIC Educational Resources Information Center

Her, Chia S.

2014-01-01

The educational experiences of Southeast Asian Americans, particularly Cambodian Americans, Hmong Americans, Laotian Americans, and Vietnamese Americans, are characterized by numerous challenges, which can be attributed to their migration history, socioeconomic status, and English proficiency. By the end of 11th grade, a high percentage of…

Reactive Attachment Disorder: Implications for School Readiness and School Functioning

ERIC Educational Resources Information Center

Schwartz, Eric; Davis, Andrew S.

2006-01-01

School readiness and functioning in children diagnosed with Reactive Attachment Disorder (RAD) are important issues due to the dramatic impact RAD has on multiple areas of development. The negative impact of impaired or disrupted early relationships, characterized by extreme neglect, abuse, parental mental illness, domestic violence, and repeated…

Are You Ready for Knowledge Sharing? An Empirical Study of Virtual Communities

ERIC Educational Resources Information Center

Hung, Shiu-Wan; Cheng, Min-Jhih

2013-01-01

This study aimed to explore the relationship between knowledge sharing intentions and the perceptions of individual technology users who are members of virtual communities. We characterized learners' perceptions of new technological products or services by including both an individual's psychological state of readiness to accept technology and…

Real-time quantitative PCR detection of genetically modified Maximizer maize and Roundup Ready soybean in some representative foods.

PubMed

Vaïtilingom, M; Pijnenburg, H; Gendre, F; Brignon, P

1999-12-01

A fast and quantitative method was developed to detect transgenic "Maximizer" maize "event 176" (Novartis) and "Roundup Ready" soybean (Monsanto) in food by real-time quantitative PCR. The use of the ABI Prism 7700 sequence detection system allowed the determination of the amplified product accumulation through a fluorogenic probe (TaqMan). Fluorescent dyes were chosen in such a way as to coamplify total and transgenic DNA in the same tube. Using real-time quantitative PCR, 2 pg of transgenic or total DNA per gram of starting sample was detected in 3 h after DNA extraction and the relative amounts of "Maximizer" maize and "Roundup Ready" soybean in some representative food products were quantified.

Prevalence of Staphylococcus aureus and Methicillin-Resistant Staphylococcus aureus in Retail Ready-to-Eat Foods in China

PubMed Central

Yang, Xiaojuan; Zhang, Jumei; Yu, Shubo; Wu, Qingping; Guo, Weipeng; Huang, Jiahui; Cai, Shuzhen

2016-01-01

Staphylococcus aureus, particularly methicillin-resistant S.aureus (MRSA), is a life-threatening pathogen in humans, and its presence in food is a public health concern. MRSA has been identified in foods in China, but little information is available regarding MRSA in ready-to-eat (RTE) foods. We aimed to investigate the prevalence of S. aureus and MRSA in Chinese retail RTE foods. All isolated S. aureus were tested for antimicrobial susceptibility, and MRSA isolates were further characterized by multilocus sequence typing (MLST) and staphylococcal cassette chromosome mec (SCCmec) typing. Of the 550 RTE foods collected from 2011 to 2014, 69 (12.5%) were positive for S. aureus. Contamination levels were mostly in the range of 0.3–10 most probable number (MPN)/g, with five samples exceeding 10 MPN/g. Of the 69 S. aureus isolates, seven were identified as MRSA by cefoxitin disc diffusion test. Six isolates were mecA-positive, while no mecC-positive isolates were identified. In total, 75.8% (47/62) of the methicillin-susceptible S. aureus isolates and all of the MRSA isolates were resistant to three or more antibiotics. Amongst the MRSA isolates, four were identified as community-acquired strains (ST59-MRSA-IVa (n = 2), ST338-MRSA-V, ST1-MRSA-V), while one was a livestock-associated strain (ST9, harboring an unreported SCCmec type 2C2). One novel sequence type was identified (ST3239), the SCCmec gene of which could not be typed. Overall, our findings showed that Chinese retail RTE foods are likely vehicles for transmission of multidrug-resistant S. aureus and MRSA lineages. This is a serious public health risk and highlights the need to implement good hygiene practices. PMID:27375562

The FLEXGene repository: exploiting the fruits of the genome projects by creating a needed resource to face the challenges of the post-genomic era.

PubMed

Brizuela, Leonardo; Richardson, Aaron; Marsischky, Gerald; Labaer, Joshua

2002-01-01

Thanks to the results of the multiple completed and ongoing genome sequencing projects and to the newly available recombination-based cloning techniques, it is now possible to build gene repositories with no precedent in their composition, formatting, and potential. This new type of gene repository is necessary to address the challenges imposed by the post-genomic era, i.e., experimentation on a genome-wide scale. We are building the FLEXGene (Full Length EXpression-ready) repository. This unique resource will contain clones representing the complete ORFeome of different organisms, including Homo sapiens as well as several pathogens and model organisms. It will consist of a comprehensive, characterized (sequence-verified), and arrayed gene repository. This resource will allow full exploitation of the genomic information by enabling genome-wide scale experimentation at the level of functional/phenotypic assays as well as at the level of protein expression, purification, and analysis. Here we describe the rationale and construction of this resource and focus on the data obtained from the Saccharomyces cerevisiae project.

Ready-to-eat street-vended food as a potential vehicle of bacterial pathogens and antimicrobial resistance: An exploratory study in Porto region, Portugal.

PubMed

Campos, Joana; Gil, Joana; Mourão, Joana; Peixe, Luísa; Antunes, Patrícia

2015-08-03

The ready-to-eat street vending commerce, as street mobile food vendors, has grown exponentially worldwide, representing in some countries a significant proportion of food consumed by the urban population. However, the microbiological food safety hazards of mobile vending units in industrialized countries are scarcely evaluated. To assess the microbiological quality and safety of this type of food and try to achieve the connection of its contamination with hygienic conditions of food-handlers, we analyzed hotdogs (n = 10), hamburgers (n = 10) and hands (n = 9) from ten street-vending trailers in the Porto region. Food and food-handler samples were tested for Enterobacteriaceae and coliform counts, Escherichia coli and coagulase-positive staphylococci counts/detection and presence of Salmonella. Aerobic mesophilic counts and detection of Listeria monocytogenes (Pulsed Field Gel Electrophoresis-PFGE and serotyping) were also tested in food samples. E. coli isolates were confirmed by MALDI-TOF and characterized for clonality (phylogenetic groups-PhG, PFGE and Multilocus Sequence Typing), antibiotic resistance (disk diffusion, PCR/sequencing) and intestinal pathogenic virulence factors (PCR/sequencing). All food samples presented poor microbiological quality (100% Enterobacteriaceae and coliforms; 20% E. coli (4 hamburgers, 4 trailers) and 20% (2 hamburgers/2 hotdogs, 3 trailers) were positive for L. monocytogenes (2 PFGE-types belonging to serotype 1/2a and 4b). Salmonella and coagulase-positive staphylococci were not detected. Food-handlers carried Enterobacteriaceae and coliforms (100%), E. coli (11%) and/or coagulase-positive staphylococci (44%). E. coli was detected in 12 samples (n = 30-food/food-handlers; phylogenetic groups A0/A1/B1) with 33% resistant to one or more antibiotics. Two multidrug resistant atypical E. coli pathotype strains (astA-ST165(CC165)/food-handler, eaeA-ST327/food) were detected. Three out of eight E. coli clonal lineages [ST409/ST976(CC10)/ST297] and the two L. monocytogenes clones were spread in different samples/trailers, suggesting cross-contamination or a common source of contamination. This exploratory study, in Porto region, showed ready-to-eat street foods from vending trailers as potential vehicles of clinically relevant L. monocytogenes serotypes and/or E. coli carrying clinically relevant virulence/antibiotic resistance features, and food-handlers as a critical risk factor in this expanding food sector. Copyright © 2015 Elsevier B.V. All rights reserved.

School Readiness amongst Urban Canadian Families: Risk Profiles and Family Mediation

ERIC Educational Resources Information Center

Browne, Dillon T.; Wade, Mark; Prime, Heather; Jenkins, Jennifer M.

2018-01-01

There is an ongoing need for literature that identifies the effects of broad contextual risk on school readiness outcomes via family mediating mechanisms. This is especially true amongst diverse and urban samples characterized by variability in immigration history. To address this limitation, family profiles of sociodemographic and contextual risk…

School-readiness profiles of children with language impairment: linkages to home and classroom experiences.

PubMed

Pentimonti, Jill M; Justice, Laura M; Kaderavek, Joan N

2014-01-01

This study represents an effort to advance our understanding of the nature of school readiness among children with language impairment (LI), a population of children acknowledged to be at risk of poor academic achievement. The academic, social-emotional, and behavioural competencies with which children arrive at kindergarten affect the nature of their future educational experiences, and their overall academic achievement. To examine whether there are reliable profiles that characterize children with LI just prior to kindergarten entrance, and the extent to which profile membership is associated with characteristics of children's homes and preschool experiences. Questions addressed were twofold: (1) To what extent are there reliable profiles of children with LI with respect to their school readiness? (2) To what extent is children's profile membership associated with characteristics of their homes and preschool classrooms? Participants were 136 children with LI from early childhood special education classrooms. We utilized latent class analysis (LCA) to classify individuals into profiles based on individual responses on school readiness measures. We then used multilevel hierarchical generalized linear models to examine the relations between profile membership and children's home/classroom experiences. LCA analyses revealed that a four-profile solution was the most appropriate fit for the data and that classroom experiences were predictive of these profiles, such that children in classrooms with more instructional/emotional support were more likely to be placed in profiles characterized by higher school readiness skills. These results suggest that the school readiness profiles of young children with LI are associated with the quality of children's classroom experiences, and that high-quality classroom experiences can be influential for ensuring that young children with LI arrive in kindergarten ready to learn. © 2014 Royal College of Speech and Language Therapists.

The Biomolecule Sequencer Project: Nanopore Sequencing as a Dual-Use Tool for Crew Health and Astrobiology Investigations

NASA Technical Reports Server (NTRS)

John, K. K.; Botkin, D. S.; Burton, A. S.; Castro-Wallace, S. L.; Chaput, J. D.; Dworkin, J. P.; Lehman, N.; Lupisella, M. L.; Mason, C. E.; Smith, D. J.;

Yersinia enterocolitica Outbreak Associated with Ready-to-Eat Salad Mix, Norway, 2011

PubMed Central

Heier, Berit Tafjord; Nygård, Karin; Stalheim, Torunn; Cudjoe, Kofitsyo S.; Skjerdal, Taran; Wester, Astrid Louise; Lindstedt, Bjørn-Arne; Stavnes, Trine-Lise; Vold, Line

2012-01-01

In 2011, an outbreak of illness caused by Yersinia enterocolitica O:9 in Norway was linked to ready-to-eat salad mix, an unusual vehicle for this pathogen. The outbreak illustrates the need to characterize isolates of this organism, and reinforces the need for international traceback mechanisms for fresh produce. PMID:22932318

Refinement of a Conceptual Model for Adolescent Readiness to Engage in End-of-Life Discussions.

PubMed

Bell, Cynthia J; Zimet, Gregory D; Hinds, Pamela S; Broome, Marion E; McDaniel, Anna M; Mays, Rose M; Champion, Victoria L

Adolescents living with incurable cancer require ongoing support to process grief, emotions, and information as disease progresses including treatment options (phase 1 clinical trials and/or hospice/palliative care). Little is known about how adolescents become ready for such discussions. The purpose of this study was to explore the process of adolescent readiness for end-of-life preparedness discussions, generating a theoretical understanding for guiding clinical conversations when curative options are limited. We explored 2 in-depth cases across time using case-study methodology. An à priori conceptual model based on current end-of-life research guided data collection and analysis. Multiple sources including in-depth adolescent interviews generated data collection on model constructs. Analysis followed a logical sequence establishing a chain of evidence linking raw data to study conclusions. Synthesis and data triangulation across cases and time led to theoretical generalizations. Initially, we proposed a linear process of readiness with 3 domains: a cognitive domain (awareness), an emotional domain (acceptance), and a behavioral domain (willingness), which preceded preparedness. Findings led to conceptual model refinement showing readiness is a dynamic internal process that interacts with preparedness. Current awareness context facilitates the type of preparedness discussions (cognitive or emotional). Furthermore, social constraint inhibits discussions. Data support theoretical understanding of the dynamism of readiness. Future research that validates adolescent conceptualization will ensure age-appropriate readiness representation. Understanding the dynamic process of readiness for engaging in end-of-life preparedness provides clinician insight for guiding discussions that facilitate shared decision making and promote quality of life for adolescents and their families.

Nonsense mutations in the PAX3 gene cause Waardenburg syndrome type I in two Chinese patients.

PubMed

Yang, Shu-Zhi; Cao, Ju-Yang; Zhang, Rui-Ning; Liu, Li-Xian; Liu, Xin; Zhang, Xin; Kang, Dong-Yang; Li, Mei; Han, Dong-Yi; Yuan, Hui-Jun; Yang, Wei-Yan

2007-01-05

Waardenburg syndrome type I (WS1) is an autosomal dominant disorder characterized by sensorineural hearing loss, pigmental abnormalities of the eye, hair and skin, and dystopia canthorum. The gene mainly responsible for WS1 is PAX3 which is involved in melanocytic development and survival. Mutations of PAX3 have been reported in familiar or sporadic patients with WS1 in several populations of the world except Chinese. In order to explore the genetic background of Chinese WS1 patients, a mutation screening of PAX3 gene was carried out in four WS1 pedigrees. A questionnaire survey and comprehensive clinical examination were conducted in four Chinese pedigrees of WS1. Genomic DNA from each patient and their family members was extracted and exons of PAX3 were amplified by PCR. PCR fragments were ethanol-purified and sequenced in both directions on an ABI_Prism 3100 DNA sequencer with the BigDye Terminator Cycle Sequencing Ready Reaction Kit. The sequences were obtained and aligned to the wild type sequence of PAX3 with the GeneTool program. Two nonsense PAX3 mutations have been found in the study population. One is heterozygous for a novel nonsense mutation S209X. The other is heterozygous for a previously reported mutation in European population R223X. Both mutations create stop codons leading to truncation of the PAX3 protein. This is the first demonstration of PAX3 mutations in Chinese WS1 patients and one of the few examples of an identical mutation of PAX3 occurred in different populations.

School readiness of children with language impairment: predicting literacy skills from pre-literacy and social-behavioural dimensions.

PubMed

Pentimonti, Jill M; Murphy, Kimberly A; Justice, Laura M; Logan, Jessica A R; Kaderavek, Joan N

2016-03-01

School readiness generally captures the notion that children do best when they arrive at formal schooling with a certain threshold of skill that will help them thrive in the classroom's academic and social milieu. To examine the dimensionality of the construct of school readiness among children with language impairment (LI), as well as the extent to which these dimensions relate to children's end-of-kindergarten literacy skills. Participants were 136 preschool-aged children with LI. Children were assessed on measures of pre-literacy, social, and behavioural skills in preschool and reading and spelling in kindergarten. Confirmatory factor analyses indicated that school readiness for this sample of children with LI is best characterized as two dimensions: pre-literacy and socio-emotional. Of the two dimensions, pre-literacy readiness was predictive of children's future performance in reading and spelling. The results further our theoretical understanding of the dimensions of school readiness, as well as our knowledge of how these skills are related among children with LI. Identifying domain-specific readiness skills that are predictive of kindergarten success can help to identify means of early assessment and targets for speech-language intervention. © 2015 Royal College of Speech and Language Therapists.

Species Distribution and Prevalence of Putative Virulence Factors in Mesophilic Aeromonas spp. Isolated from Fresh Retail Sushi

PubMed Central

Hoel, Sunniva; Vadstein, Olav; Jakobsen, Anita N.

2017-01-01

Aeromonas spp. are ubiquitous bacteria that have received increasing attention as human pathogens because of their widespread occurrence in food, especially seafood and vegetables. The aim of this work was to assess the species identity and phylogenetic relationship of 118 Aeromonas strains isolated from fresh retail sushi from three producers, and to characterize the isolates with respect to genetic and phenotypic virulence factors. We also evaluate the potential hazard associated with their presence in ready-to-eat seafood not subjected to heat treatment. Mesophilic Aeromonas salmonicida was most prevalent (74%), followed by A. bestiarum (9%), A. dhakensis (5%), A. caviae (5%), A. media (4%), A. hydrophila (2%), and A. piscicola (1%). All isolates were considered potentially pathogenic due to the high prevalence of genes encoding hemolysin (hlyA) (99%), aerolysin (aerA) (98%), cytotoxic enterotoxin (act) (86%), heat-labile cytotonic enterotoxin (alt) (99%), and heat-stable cytotonic enterotoxin (ast) (31%). The shiga-like toxins 1 and 2 (stx-1 and stx-2) were not detected. Moreover, there was heterogeneity in toxin gene distribution among the isolates, and the combination of act/alt/hlyA/aerA was most commonly detected (63%). β-hemolysis was species-dependent and observed in 91% of the isolates. All A. media and A. caviae strains were non-hemolytic. For isolates belonging to this group, lack of hemolysis was possibly related to the absence of the act gene. Swimming motility, linked to adhesion and host invasion, occurred in 65% of the isolates. Partial sequencing of the gyrB gene demonstrated its suitability as a genetic marker for Aeromonas species identification and for assessment of the phylogenetic relationship between the isolates. The gyrB sequence divergence within a given species ranged from 1.3 to 2.9%. A. bestiarum, A. salmonicida, and A. piscicola were the most closely related species; their sequences differed by 2.7–3.4%. The average gyrB sequence similarity between all species was 93%, demonstrating its acceptable taxonomic resolution. The presence of multiple species of potential pathogenic Aeromonas in fresh retail sushi raises new food safety issues related to the increased consumption of ready-to-eat food composed of raw ingredients. PMID:28596762

Potential risk of norovirus infection due to the consumption of "ready to eat" food.

PubMed

Serracca, Laura; Rossini, Irene; Battistini, Roberta; Goria, Maria; Sant, Serena; De Montis, Gabriella; Ercolini, Carlo

2012-09-01

In this study, we investigated the presence of enteric viruses such as norovirus (NoV), hepatitis A virus (HAV), hepatitis E virus (HEV), and adenovirus (HAdV), in vegetables available on the Italian markets. For this aim, 110 national and international "ready to eat" samples were collected and analyzed by biomolecular tests and positive samples were confirmed by sequencing. All samples (100 %) were negative for HAV, HEV, and HAdV, while 13.6 % (15/110) were positive for NoV. Actually there is not a formal surveillance system for NoV infections in Italy but we clearly demonstrated a potential risk associated with the consumption of "ready to eat" vegetables. This study confirmed for the first time in Italy the presence of norovirus in semi-dried tomatoes by PCR technique.

Company profile: Complete Genomics Inc.

PubMed

Reid, Clifford

2011-02-01

Complete Genomics Inc. is a life sciences company that focuses on complete human genome sequencing. It is taking a completely different approach to DNA sequencing than other companies in the industry. Rather than building a general-purpose platform for sequencing all organisms and all applications, it has focused on a single application - complete human genome sequencing. The company's Complete Genomics Analysis Platform (CGA™ Platform) comprises an integrated package of biochemistry, instrumentation and software that sequences human genomes at the highest quality, lowest cost and largest scale available. Complete Genomics offers a turnkey service that enables customers to outsource their human genome sequencing to the company's genome sequencing center in Mountain View, CA, USA. Customers send in their DNA samples, the company does all the library preparation, DNA sequencing, assembly and variant analysis, and customers receive research-ready data that they can use for biological discovery.

WIPP Remote-Handled TRU Waste Program Update

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

Most, W.; Kehrman, B.

2006-07-01

There are two major regulatory approval milestones necessary in order to commence disposal operations for remote-handled transuranic (RH TRU) waste at the Waste Isolation Pilot Plant (WIPP)-the RH TRU hazardous waste permit modification request [1] and the radiological characterization plan [2]. One of those milestones has been achieved. The US Environmental Protection Agency (EPA) issued its final decision to approve the Department of Energy's (DOE) RH TRU radiological characterization plan along with the RH TRU Waste Characterization Program Implementation Plan [3], on March 26, 2004. The RH TRU hazardous waste permit modification request still awaits agency approval. In EPA's decisionmore » to approve the DOE's RH TRU radiological characterization plan, the EPA also set forth the process for approving site-specific RH TRU waste characterization programs. Included in the March 29, 2005, RH TRU second Notice of Deficiency [4] (NOD) on the Class 3 Permit Modification Request for RH TRU Waste, the New Mexico Environment Department (NMED) requested that the Permittees combine their responses for the RH TRU Waste NOD with the Section 311 permit modification request NOD. The Combined Response Document was submitted April 28, 2005 [5]. Another NOD [6] was issued by the NMED on September 1, 2005, to clarify the Permittees' proposal and submit these clarifications to the administrative record. Combining both the chap. 311 [7] and RH TRU waste permit modification requests allows for both the regulator and Permittees to expedite action on the modification requests. The Combined Response Document preserves human resources and costs by having only one administrative process for both modification requests. Facility readiness requirements of the RH TRU waste final permit [8] must be implemented to declare that the WIPP is ready to receive RH TRU waste for storage and disposal. To demonstrate readiness, the WIPP is preparing for an Operational Readiness Review (ORR) of the RH TRU waste management equipment, system, and procedures. Required by DOE Order, the ORR demonstrates the capability of managing RH TRU waste. The Management and Operating Contractor (MOC) for the WIPP must first perform a Line Management Assessment. Upon successful completion of the Line Management Assessment, the MOC performs the Contractor ORR and presents the results to the local DOE office. At that time, the local DOE office performs its own ORR to declare readiness to DOE Headquarters. (authors)« less

Two sequence-ready contigs spanning the two copies of a 200-kb duplication on human 21q: partial sequence and polymorphisms.

PubMed

Potier, M; Dutriaux, A; Orti, R; Groet, J; Gibelin, N; Karadima, G; Lutfalla, G; Lynn, A; Van Broeckhoven, C; Chakravarti, A; Petersen, M; Nizetic, D; Delabar, J; Rossier, J

1998-08-01

Physical mapping across a duplication can be a tour de force if the region is larger than the size of a bacterial clone. This was the case of the 170- to 275-kb duplication present on the long arm of chromosome 21 in normal human at 21q11.1 (proximal region) and at 21q22.1 (distal region), which we described previously. We have constructed sequence-ready contigs of the two copies of the duplication of which all the clones are genuine representatives of one copy or the other. This required the identification of four duplicon polymorphisms that are copy-specific and nonallelic variations in the sequence of the STSs. Thirteen STSs were mapped inside the duplicated region and 5 outside but close to the boundaries. Among these STSs 10 were end clones from YACs, PACs, or cosmids, and the average interval between two markers in the duplicated region was 16 kb. Eight PACs and cosmids showing minimal overlaps were selected in both copies of the duplication. Comparative sequence analysis along the duplication showed three single-basepair changes between the two copies over 659 bp sequenced (4 STSs), suggesting that the duplication is recent (less than 4 mya). Two CpG islands were located in the duplication, but no genes were identified after a 36-kb cosmid from the proximal copy of the duplication was sequenced. The homology of this chromosome 21 duplicated region with the pericentromeric regions of chromosomes 13, 2, and 18 suggests that the mechanism involved is probably similar to pericentromeric-directed mechanisms described in interchromosomal duplications. Copyright 1998 Academic Press.

Digital gene expression analysis with sample multiplexing and PCR duplicate detection: A straightforward protocol.

PubMed

Rozenberg, Andrey; Leese, Florian; Weiss, Linda C; Tollrian, Ralph

2016-01-01

Tag-Seq is a high-throughput approach used for discovering SNPs and characterizing gene expression. In comparison to RNA-Seq, Tag-Seq eases data processing and allows detection of rare mRNA species using only one tag per transcript molecule. However, reduced library complexity raises the issue of PCR duplicates, which distort gene expression levels. Here we present a novel Tag-Seq protocol that uses the least biased methods for RNA library preparation combined with a novel approach for joint PCR template and sample labeling. In our protocol, input RNA is fragmented by hydrolysis, and poly(A)-bearing RNAs are selected and directly ligated to mixed DNA-RNA P5 adapters. The P5 adapters contain i5 barcodes composed of sample-specific (moderately) degenerate base regions (mDBRs), which later allow detection of PCR duplicates. The P7 adapter is attached via reverse transcription with individual i7 barcodes added during the amplification step. The resulting libraries can be sequenced on an Illumina sequencer. After sample demultiplexing and PCR duplicate removal with a free software tool we designed, the data are ready for downstream analysis. Our protocol was tested on RNA samples from predator-induced and control Daphnia microcrustaceans.

EIA's Natural Gas Production Data

EIA Publications

2009-01-01

This special report examines the stages of natural gas processing from the wellhead to the pipeline network through which the raw product becomes ready for transportation and eventual consumption, and how this sequence is reflected in the data published by the Energy Information Administration (EIA).

Social networks and community prevention coalitions.

PubMed

Feinberg, Mark E; Riggs, Nathaniel R; Greenberg, Mark T

2005-07-01

This study investigates the links between community readiness and the social networks among participants in Communities That Care (CTC), community-based prevention coalitions. The coalitions targeted adolescent behavior problems through community risk factor assessments, prioritization of risk factors, and selection/implementation of corresponding evidence-based family, school, and community programs. Key leaders (n = 219) in 23 new CTC sites completed questionnaires focusing on community readiness to implement CTC and the respondents' personal, work, and social organization links to other key leaders in the community. Outside technical assistants also completed ratings of each community's readiness and early CTC functioning. Measures of network cohesion/integration were positively associated with readiness, while centralization was negatively associated. These results suggest that non-centralized networks in which ties between members are close and direct may be an indicator of community readiness. In addition, we found different associations between readiness and different domains of social relations. EDITORS' STRATEGIC IMPLICATIONS: The authors present the promising practice of using social network analysis to characterize the functioning of local prevention coalitions and their readiness to implement a community-based prevention initiative. Researchers and community planners will benefit from the lessons in this article, which capitalizes on a large sample and multiple informants. This work raises interesting questions about how to combine the promotion of coalition functioning while simultaneously encouraging diversity of coalition membership.

A Model and Algorithms For a Software Evolution Control System

DTIC Science & Technology

1993-12-01

dynamic scheduling approaches can be found in [67). Task scheduling can also be characterized as preemptive and nonpreemptive . A task is preemptive ...is NP-hard for both the preemptive and nonpreemptive cases [671 [84). Scheduling nonpreemptive tasks with arbitrary ready times is NP-hard in both...the preemptive and nonpreemptive cases [671 [841. Scheduling nonpreemptive tasks with arbitrary ready times is NP-hard in both multiprocessor and

A Module Experimental Process System Development Unit (MEPSDU)

NASA Technical Reports Server (NTRS)

1982-01-01

Restructuring research objectives from a technical readiness demonstration program to an investigation of high risk, high payoff activities associated with producing photovoltaic modules using non-CZ sheet material is reported. Deletion of the module frame in favor of a frameless design, and modification in cell series parallel electrical interconnect configuration are reviewed. A baseline process sequence was identified for the fabrication of modules using the selected dendritic web sheet material, and economic evaluations of the sequence were completed.

A platform for efficient genotyping in Musa using microsatellite markers

PubMed Central

Christelová, Pavla; Valárik, Miroslav; Hřibová, Eva; Van den houwe, Ines; Channelière, Stéphanie; Roux, Nicolas; Doležel, Jaroslav

2011-01-01

Background and aims Bananas and plantains (Musa spp.) are one of the major fruit crops worldwide with acknowledged importance as a staple food for millions of people. The rich genetic diversity of this crop is, however, endangered by diseases, adverse environmental conditions and changed farming practices, and the need for its characterization and preservation is urgent. With the aim of providing a simple and robust approach for molecular characterization of Musa species, we developed an optimized genotyping platform using 19 published simple sequence repeat markers. Methodology The genotyping system is based on 19 microsatellite loci, which are scored using fluorescently labelled primers and high-throughput capillary electrophoresis separation with high resolution. This genotyping platform was tested and optimized on a set of 70 diploid and 38 triploid banana accessions. Principal results The marker set used in this study provided enough polymorphism to discriminate between individual species, subspecies and subgroups of all accessions of Musa. Likewise, the capability of identifying duplicate samples was confirmed. Based on the results of a blind test, the genotyping system was confirmed to be suitable for characterization of unknown accessions. Conclusions Here we report on the first complex and standardized platform for molecular characterization of Musa germplasm that is ready to use for the wider Musa research and breeding community. We believe that this genotyping system offers a versatile tool that can accommodate all possible requirements for characterizing Musa diversity, and is economical for samples ranging from one to many accessions. PMID:22476494

Comparative genomics analyses revealed two virulent Listeria monocytogenes strains isolated from ready-to-eat food.

PubMed

Lim, Shu Yong; Yap, Kien-Pong; Thong, Kwai Lin

2016-01-01

Listeria monocytogenes is an important foodborne pathogen that causes considerable morbidity in humans with high mortality rates. In this study, we have sequenced the genomes and performed comparative genomics analyses on two strains, LM115 and LM41, isolated from ready-to-eat food in Malaysia. The genome size of LM115 and LM41 was 2,959,041 and 2,963,111 bp, respectively. These two strains shared approximately 90% homologous genes. Comparative genomics and phylogenomic analyses revealed that LM115 and LM41 were more closely related to the reference strains F2365 and EGD-e, respectively. Our virulence profiling indicated a total of 31 virulence genes shared by both analysed strains. These shared genes included those that encode for internalins and L. monocytogenes pathogenicity island 1 (LIPI-1). Both the Malaysian L. monocytogenes strains also harboured several genes associated with stress tolerance to counter the adverse conditions. Seven antibiotic and efflux pump related genes which may confer resistance against lincomycin, erythromycin, fosfomycin, quinolone, tetracycline, and penicillin, and macrolides were identified in the genomes of both strains. Whole genome sequencing and comparative genomics analyses revealed two virulent L. monocytogenes strains isolated from ready-to-eat foods in Malaysia. The identification of strains with pathogenic, persistent, and antibiotic resistant potentials from minimally processed food warrant close attention from both healthcare and food industry.

Design of integration-ready metasurface-based infrared absorbers

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

Ogando, Karim, E-mail: karim@cab.cnea.gov.ar; Pastoriza, Hernán

2015-07-28

We introduce an integration ready design of metamaterial infrared absorber, highly compatible with many kinds of fabrication processes. We present the results of an exhaustive experimental characterization, including an analysis of the effects of single meta-atom geometrical parameters and collective arrangement. We confront the results with the theoretical interpretations proposed in the literature. Based on the results, we develop a set of practical design rules for metamaterial absorbers in the infrared region.

SONAR: A High-Throughput Pipeline for Inferring Antibody Ontogenies from Longitudinal Sequencing of B Cell Transcripts.

PubMed

Schramm, Chaim A; Sheng, Zizhang; Zhang, Zhenhai; Mascola, John R; Kwong, Peter D; Shapiro, Lawrence

2016-01-01

The rapid advance of massively parallel or next-generation sequencing technologies has made possible the characterization of B cell receptor repertoires in ever greater detail, and these developments have triggered a proliferation of software tools for processing and annotating these data. Of especial interest, however, is the capability to track the development of specific antibody lineages across time, which remains beyond the scope of most current programs. We have previously reported on the use of techniques such as inter- and intradonor analysis and CDR3 tracing to identify transcripts related to an antibody of interest. Here, we present Software for the Ontogenic aNalysis of Antibody Repertoires (SONAR), capable of automating both general repertoire analysis and specialized techniques for investigating specific lineages. SONAR annotates next-generation sequencing data, identifies transcripts in a lineage of interest, and tracks lineage development across multiple time points. SONAR also generates figures, such as identity-divergence plots and longitudinal phylogenetic "birthday" trees, and provides interfaces to other programs such as DNAML and BEAST. SONAR can be downloaded as a ready-to-run Docker image or manually installed on a local machine. In the latter case, it can also be configured to take advantage of a high-performance computing cluster for the most computationally intensive steps, if available. In summary, this software provides a useful new tool for the processing of large next-generation sequencing datasets and the ontogenic analysis of neutralizing antibody lineages. SONAR can be found at https://github.com/scharch/SONAR, and the Docker image can be obtained from https://hub.docker.com/r/scharch/sonar/.

Readiness for change and job satisfaction in a case of lean management application - a comparative study.

PubMed

Lipińska-Grobelny, Agnieszka; Papieska, Ewelina

2012-09-01

This current study investigates the effect of lean management system on work attitudes of workers of two manufacturing companies. "Lean management" is a concept of work processes and human relations that determines company's productivity and profitability. Workers of two enterprises, the first one with lean production and the second one with old mass production, were compared for their readiness for change and job satisfaction (both emotional and cognitive aspect). The sample of 102 employees completed a battery of instruments such as: the Job Description Inventory by Neuberger and Allerbeck, the Job Affect Scale by Burke et al. and the Change-Readiness Scale by Kriegel and Brandt. Individuals from the lean manufacturing company were characterized by higher level of readiness for change, positive affect at work, and cognitive job satisfaction. In this approach the introduction of lean production positively affected company's human resource attitudes.

A Primer on Adventure Education in the Camp Setting.

ERIC Educational Resources Information Center

Nei, Eric

2003-01-01

Basic concepts of experiential learning theory are presented to assist camp directors in choosing knowledgeable staff and developing successful adventure programs. These concepts include assessment of learner (camper) readiness, activity sequencing, learning cycle, comfort zone, activity framing, task goals versus process goals, and five stages of…

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

PubMed Central

Morgan, Martin; Anders, Simon; Lawrence, Michael; Aboyoun, Patrick; Pagès, Hervé; Gentleman, Robert

2009-01-01

Summary: ShortRead is a package for input, quality assessment, manipulation and output of high-throughput sequencing data. ShortRead is provided in the R and Bioconductor environments, allowing ready access to additional facilities for advanced statistical analysis, data transformation, visualization and integration with diverse genomic resources. Availability and Implementation: This package is implemented in R and available at the Bioconductor web site; the package contains a ‘vignette’ outlining typical work flows. Contact: mtmorgan@fhcrc.org PMID:19654119

Draft Genome Sequence of Vancomycin-Heteroresistant Staphylococcus epidermidis Strain UC7032, Isolated from Food

PubMed Central

Pietta, Ester; Bassi, Daniela; Fontana, Cecilia; Puglisi, Edoardo; Cappa, Fabrizio; Cocconcelli, Pier Sandro

2013-01-01

Staphylococcus epidermidis strain UC7032 was isolated from ready-to-eat cured meat and is heteroresistant to glycopeptide antibiotics. The draft whole-genome analysis revealed that this strain shows common characteristics typical of strains that are involved in nosocomial infections. PMID:24072859

Enhancement of Educational Effect Through Extensive and Intensive Intervention--The Gulfport Project.

ERIC Educational Resources Information Center

Goolsby, Thomas M., Jr.; Frary, Robert B.

Two hundred first grade children participated in an experimental program involving innovative curricula and instructional techniques. A pretest-posttest method of instruction, employing sequenced and structured learning activities, enabled each child to progress at an individual rate and was supplemented by a readiness program. Evaluation of the…

Procedures for Empirical Determination of En-Route Criterion Levels.

ERIC Educational Resources Information Center

Moncrief, Michael H.

En-route Criterion Levels (ECLs) are defined as decision rules for predicting pupil readiness to advance through an instructional sequence. This study investigated the validity of present ELCs in an individualized mathematics program and tested procedures for empirically determining optimal ECLs. Retest scores and subsequent progress were…

Challenges in Assessing for Postsecondary Readiness

ERIC Educational Resources Information Center

Mellard, Daryl F.; Anderson, Gretchen

2007-01-01

Adult secondary education learners approach the goal of college-level postsecondary education through three assessment gateways: (a) measures of adult education program learning gains, (b) a high-school equivalency exam, and (c) college placement tests. On the surface, the assessments in this sequence might appear to work in concert and point…

Automated Array Assembly, Phase 2. Low-cost Solar Array Project, Task 4

NASA Technical Reports Server (NTRS)

Lopez, M.

1978-01-01

Work was done to verify the technological readiness of a select process sequence with respect to satisfying the Low Cost Solar Array Project objectives of meeting the designated goals of $.50 per peak watt in 1986 (1975 dollars). The sequence examined consisted of: (1) 3 inches diameter as-sawn Czochralski grown 1:0:0 silicon, (2) texture etching, (3) ion implanting, (4) laser annealing, (5) screen printing of ohmic contacts and (6) sprayed anti-reflective coatings. High volume production projections were made on the selected process sequence. Automated processing and movement of hardware at high rates were conceptualized to satisfy the PROJECT's 500 MW/yr capability. A production plan was formulated with flow diagrams integrating the various processes in the cell fabrication sequence.

MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in Metazoa.

PubMed

Catalano, Domenico; Licciulli, Flavio; Turi, Antonio; Grillo, Giorgio; Saccone, Cecilia; D'Elia, Domenica

2006-01-24

Mitochondria are sub-cellular organelles that have a central role in energy production and in other metabolic pathways of all eukaryotic respiring cells. In the last few years, with more and more genomes being sequenced, a huge amount of data has been generated providing an unprecedented opportunity to use the comparative analysis approach in studies of evolution and functional genomics with the aim of shedding light on molecular mechanisms regulating mitochondrial biogenesis and metabolism. In this context, the problem of the optimal extraction of representative datasets of genomic and proteomic data assumes a crucial importance. Specialised resources for nuclear-encoded mitochondria-related proteins already exist; however, no mitochondrial database is currently available with the same features of MitoRes, which is an update of the MitoNuc database extensively modified in its structure, data sources and graphical interface. It contains data on nuclear-encoded mitochondria-related products for any metazoan species for which this type of data is available and also provides comprehensive sequence datasets (gene, transcript and protein) as well as useful tools for their extraction and export. MitoRes http://www2.ba.itb.cnr.it/MitoRes/ consolidates information from publicly external sources and automatically annotates them into a relational database. Additionally, it also clusters proteins on the basis of their sequence similarity and interconnects them with genomic data. The search engine and sequence management tools allow the query/retrieval of the database content and the extraction and export of sequences (gene, transcript, protein) and related sub-sequences (intron, exon, UTR, CDS, signal peptide and gene flanking regions) ready to be used for in silico analysis. The tool we describe here has been developed to support lab scientists and bioinformaticians alike in the characterization of molecular features and evolution of mitochondrial targeting sequences. The way it provides for the retrieval and extraction of sequences allows the user to overcome the obstacles encountered in the integrative use of different bioinformatic resources and the completeness of the sequence collection allows intra- and interspecies comparison at different biological levels (gene, transcript and protein).

Characterizing emissions from open burning of military food waste and ration packaging compositions

EPA Science Inventory

Emissions from open burning of Meals, Ready-To-Eat (MRE) and MRE packaging were characterized in response to inhalation concerns at military forward operating bases. Emissions from four compositions of MREs and four types of packaging were compared to assess contributions of ind...

Simultaneous activation of parallel sensory pathways promotes a grooming sequence in Drosophila

PubMed Central

Hampel, Stefanie; McKellar, Claire E

2017-01-01

A central model that describes how behavioral sequences are produced features a neural architecture that readies different movements simultaneously, and a mechanism where prioritized suppression between the movements determines their sequential performance. We previously described a model whereby suppression drives a Drosophila grooming sequence that is induced by simultaneous activation of different sensory pathways that each elicit a distinct movement (Seeds et al., 2014). Here, we confirm this model using transgenic expression to identify and optogenetically activate sensory neurons that elicit specific grooming movements. Simultaneous activation of different sensory pathways elicits a grooming sequence that resembles the naturally induced sequence. Moreover, the sequence proceeds after the sensory excitation is terminated, indicating that a persistent trace of this excitation induces the next grooming movement once the previous one is performed. This reveals a mechanism whereby parallel sensory inputs can be integrated and stored to elicit a delayed and sequential grooming response. PMID:28887878

Can genomics deliver climate-change ready crops?

PubMed

Varshney, Rajeev K; Singh, Vikas K; Kumar, Arvind; Powell, Wayne; Sorrells, Mark E

2018-04-20

Development of climate resilient crops with accelerating genetic gains in crops will require integration of different disciplines/technologies, to see the impact in the farmer's field. In this review, we summarize how we are utilizing our germplasm collections to identify superior alleles/haplotypes through NGS based sequencing approaches and how genomics-enabled technologies together with precise phenotyping are being used in crop breeding. Pre-breeding and genomics-assisted breeding approaches are contributing to the more efficient development of climate-resilient crops. It is anticipated that the integration of several disciplines/technologies will result in the delivery of climate change ready crops in less time. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Evaluation of the Persistence of Infectious Human Noroviruses on Food Surfaces by Using Real-Time Nucleic Acid Sequence-Based Amplification▿

PubMed Central

Lamhoujeb, Safaa; Fliss, Ismail; Ngazoa, Solange E.; Jean, Julie

2008-01-01

Noroviruses (NoV) are the major cause of nonbacterial gastroenteritis. However, there is no published study to ascertain their survival on foodstuffs which are directly related to human health risk. In the present study, we developed a rapid, simple, and sensitive real-time nucleic acid sequence-based amplification (NASBA) combined with an enzymatic treatment for distinguishing infectious from noninfectious human NoV. The developed method was validated using spiked ready-to-eat food samples. When feline calicivirus (FCV) was used as a NoV surrogate in the preliminary assays, it appeared more sensitive to heat inactivation and enzymatic pretreatment than the human NoV. This suggests that FCV may not be an ideal model for studying NoV. Our results reveal clearly that the developed enzymatic pretreatment/real-time NASBA combination successfully distinguished the infectious from heat-inactivated NoV. Moreover, we demonstrate that NoV survived for at least 10 days on refrigerated ready-to-eat foods, such as lettuce and turkey. However, the survival rate was higher on turkey than on lettuce, probably because of their different surface natures. The approach developed in this study may be suitable for more in-depth studies of the persistence and inactivation of human NoV and may be applied to other nonculturable RNA viruses. Moreover, the evaluation of infectious NoV survival provided valuable information concerning its persistence on ready-to-eat food. PMID:18378643

G-Anchor: a novel approach for whole-genome comparative mapping utilizing evolutionary conserved DNA sequences.

PubMed

Lenis, Vasileios Panagiotis E; Swain, Martin; Larkin, Denis M

2018-05-01

Cross-species whole-genome sequence alignment is a critical first step for genome comparative analyses, ranging from the detection of sequence variants to studies of chromosome evolution. Animal genomes are large and complex, and whole-genome alignment is a computationally intense process, requiring expensive high-performance computing systems due to the need to explore extensive local alignments. With hundreds of sequenced animal genomes available from multiple projects, there is an increasing demand for genome comparative analyses. Here, we introduce G-Anchor, a new, fast, and efficient pipeline that uses a strictly limited but highly effective set of local sequence alignments to anchor (or map) an animal genome to another species' reference genome. G-Anchor makes novel use of a databank of highly conserved DNA sequence elements. We demonstrate how these elements may be aligned to a pair of genomes, creating anchors. These anchors enable the rapid mapping of scaffolds from a de novo assembled genome to chromosome assemblies of a reference species. Our results demonstrate that G-Anchor can successfully anchor a vertebrate genome onto a phylogenetically related reference species genome using a desktop or laptop computer within a few hours and with comparable accuracy to that achieved by a highly accurate whole-genome alignment tool such as LASTZ. G-Anchor thus makes whole-genome comparisons accessible to researchers with limited computational resources. G-Anchor is a ready-to-use tool for anchoring a pair of vertebrate genomes. It may be used with large genomes that contain a significant fraction of evolutionally conserved DNA sequences and that are not highly repetitive, polypoid, or excessively fragmented. G-Anchor is not a substitute for whole-genome aligning software but can be used for fast and accurate initial genome comparisons. G-Anchor is freely available and a ready-to-use tool for the pairwise comparison of two genomes.

Relating Resources to Personnel Readiness. Use of Army Strength Management Models,

DTIC Science & Technology

1997-01-01

far from the resources. In fact, they do not consider them. What they do consider is the historical performance of response variables, using a...hierarchy is the readiness of the force or the ability of the overall force to perform a given mission successfully. A force is composed of units...at the unit level. SORTS pro- duces unit "C-levels" that characterize the proportion of the wartime mission the unit can perform .5 Separate ratings

Rapid in vivo apparent diffusion coefficient mapping of hyperpolarized (13) C metabolites.

PubMed

Koelsch, Bertram L; Reed, Galen D; Keshari, Kayvan R; Chaumeil, Myriam M; Bok, Robert; Ronen, Sabrina M; Vigneron, Daniel B; Kurhanewicz, John; Larson, Peder E Z

2015-09-01

Hyperpolarized (13) C magnetic resonance allows for the study of real-time metabolism in vivo, including significant hyperpolarized (13) C lactate production in many tumors. Other studies have shown that aggressive and highly metastatic tumors rapidly transport lactate out of cells. Thus, the ability to not only measure the production of hyperpolarized (13) C lactate but also understand its compartmentalization using diffusion-weighted MR will provide unique information for improved tumor characterization. We used a bipolar, pulsed-gradient, double spin echo imaging sequence to rapidly generate diffusion-weighted images of hyperpolarized (13) C metabolites. Our methodology included a simultaneously acquired B1 map to improve apparent diffusion coefficient (ADC) accuracy and a diffusion-compensated variable flip angle scheme to improve ADC precision. We validated this sequence and methodology in hyperpolarized (13) C phantoms. Next, we generated ADC maps of several hyperpolarized (13) C metabolites in a normal rat, rat brain tumor, and prostate cancer mouse model using both preclinical and clinical trial-ready hardware. ADC maps of hyperpolarized (13) C metabolites provide information about the localization of these molecules in the tissue microenvironment. The methodology presented here allows for further studies to investigate ADC changes due to disease state that may provide unique information about cancer aggressiveness and metastatic potential. © 2014 Wiley Periodicals, Inc.

"Shovel-ready" Sequences as a Stimulus for the Next Generation of Life Scientists.

PubMed

Boyle, Michael D

2010-01-01

Genomics and bioinformatics are dynamic fields well-suited for capturing the imagination of undergraduates in both research laboratories and classrooms. Currently, raw nucleotide sequence is being provided, as part of several genomics research initiatives, for undergraduate research and teaching. These initiatives could be easily extended and much more effective if the source of the sequenced material and the subsequent focus of the data analysis were aligned with the research interests of individual faculty at undergraduate institutions. By judicious use of surplus capacity in existing nucleotide sequencing cores, raw sequence data could be generated to support ongoing research efforts involving undergraduates. This would allow these students to participate actively in discovery research, with a goal of making novel contributions to their field through original research while nurturing the next generation of talented research scientists.

Delay discounting and intake of ready-to-eat and away-from-home foods in overweight and obese women.

PubMed

Appelhans, Bradley M; Waring, Molly E; Schneider, Kristin L; Pagoto, Sherry L; DeBiasse, Michelle A; Debiasse, Michelle A; Whited, Matthew C; Lynch, Elizabeth B

2012-10-01

A shift from home-prepared to away-from-home and ready-to-eat foods has occurred in recent decades, which has implications for obesity and health. This study tested whether delay discounting, a facet of impulsivity reflecting sensitivity to immediate reward, is associated with the frequency of consumption and typical amount consumed of home-prepared, away-from-home, and ready-to-eat foods among overweight and obese women. Seventy-eight participants completed a binary choice task assessing discounting of delayed monetary rewards. Nutrient analysis of weighed food records characterized dietary intake over seven consecutive days. Foods were categorized as home-prepared, away-from-home, or ready-to-eat by a registered dietitian from information provided by participants. Delay discounting was not associated with the frequency of consuming home-prepared, away-from-home, and ready-to-eat foods as reflected in the percentages of recorded foods or total energy intake from each category. However, once consuming away-from-home and ready-to-eat foods (but not home-prepared foods), impulsive women consumed more energy than less impulsive women. Exploratory analyses indicated that more impulsive women chose away-from-home foods with a higher energy density (kcal/g). Impulsivity was associated with the quantity of away-from-home and ready-to-eat foods consumed, but not the frequency of their consumption. Home food preparation may be critical to weight control for impulsive individuals. Copyright © 2012 Elsevier Ltd. All rights reserved.

Delay discounting and intake of ready-to-eat and away-from-home foods in overweight and obese women

PubMed Central

Appelhans, Bradley M.; Waring, Molly E.; Schneider, Kristin L.; Pagoto, Sherry L.; DeBiasse, Michelle A.; Whited, Matthew C.; Lynch, Elizabeth B.

2012-01-01

A shift from home-prepared to away-from-home and ready-to-eat foods has occurred in recent decades, which has implications for obesity and health. This study tested whether delay discounting, a facet of impulsivity reflecting sensitivity to immediate reward, is associated with the frequency of consumption and typical amount consumed of home-prepared, away-from-home, and ready-to-eat foods among overweight and obese women. Seventy-eight participants completed a binary choice task assessing discounting of delayed monetary rewards. Nutrient analysis of weighed food records characterized dietary intake over seven consecutive days. Foods were categorized as home-prepared, away-from-home, or ready-to-eat by a registered dietitian from information provided by participants. Delay discounting was not associated with the frequency of consuming home-prepared, away-from-home, and ready-to-eat foods as reflected in the percentages of recorded foods or total energy intake from each category. However, once consuming away-from-home and ready-to-eat foods (but not home-prepared foods), impulsive women consumed more energy than less impulsive women. Exploratory analyses indicated that more impulsive women chose away-from-home foods with a higher energy density (kcal/g). Impulsivity was associated with the quantity of away-from-home and ready-to-eat foods consumed, but not the frequency of their consumption. Home food preparation may be critical to weight control for impulsive individuals. PMID:22819735

Determining If Phylogenetic Relatedness of Listeria Monocytogenes Isolates Corresponds to Persistence in Poultry Processing Plants Using Whole-Genome Sequencing

USDA-ARS?s Scientific Manuscript database

Introduction: Controlling Listeria monocytogenes on ready-to-eat meat and poultry products and in food processing facilities is challenging. Surveys have found that some L. monocytogenes types are more persistent in processing facilities than others, but the reason is unknown. It is possible persist...

Facing the World. An Independent Living/Pre-Employment Curriculum for Refugee Youths.

ERIC Educational Resources Information Center

Bateman, Mary Jo; And Others

This document, a curriculum guide focusing on both independent living skills and job readiness skills, is based on the experience of the Bilingual Vocational Education program in Virginia. The lessons are sequenced to increase in difficulty as students acquire more English skills, but individual units do not necessarily require competencies…

Rigorous Tests of Student Outcomes in CTE Programs of Study: Final Report

ERIC Educational Resources Information Center

Castellano, Marisa; Sundell, Kirsten E.; Overman, Laura T.; Richardson, George B.; Stone, James R., III

2014-01-01

This study was designed to investigate the relationship between participation in federally mandated college and career-preparatory programs--known as programs of study (POS)--and high school achievement outcomes. POS are an organized approach to college and career readiness that offer an aligned sequence of courses spanning secondary and…

Flow chemistry kinetic studies reveal reaction conditions for ready access to unsymmetrical trehalose analogues.

PubMed

Patel, Mitul K; Davis, Benjamin G

2010-10-07

Monofunctionalization of trehalose, a widely-found symmetric plant disaccharide, was studied in a microreactor to give valuable kinetic insights that have allowed improvements in desymmetrization yields and the development of a reaction sequence for large scale monofunctionalizations that allow access to probes of trehalose's biological function.

CHALLENGES FOR IMPLEMENTING A PTSD PREVENTIVE GENOMIC SEQUENCING PROGRAM IN THE U.S. MILITARY

PubMed Central

Lázaro-Muñoz, Gabriel; Juengst, Eric T.

2015-01-01

There is growing interest in using the quickly developing field of genomics to contribute to military readiness and effectiveness. Specifically, influential military advisory panels have recommended that the U.S. military apply genomics to help treat, prevent, or minimize the risk for post-traumatic stress disorder (PTSD) among service members. This article highlights some important scientific, legal, and ethical challenges regarding the development and deployment of a preventive genomic sequencing (PGS) program to predict the risk of PTSD among military service members. PMID:26401056

DES Science Portal: II- Creating Science-Ready Catalogs

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

Fausti Neto, Angelo; et al.

We present a novel approach for creating science-ready catalogs through a software infrastructure developed for the Dark Energy Survey (DES). We integrate the data products released by the DES Data Management and additional products created by the DES collaboration in an environment known as DES Science Portal. Each step involved in the creation of a science-ready catalog is recorded in a relational database and can be recovered at any time. We describe how the DES Science Portal automates the creation and characterization of lightweight catalogs for DES Year 1 Annual Release, and show its flexibility in creating multiple catalogs withmore » different inputs and configurations. Finally, we discuss the advantages of this infrastructure for large surveys such as DES and the Large Synoptic Survey Telescope. The capability of creating science-ready catalogs efficiently and with full control of the inputs and configurations used is an important asset for supporting science analysis using data from large astronomical surveys.« less

“Ready-to-Recruit” or “Ready-to-Consent” Populations?: Informed Consent and the Limits of Subject Autonomy

PubMed Central

Fisher, Jill A.

2011-01-01

This paper queries the pharmaceutical industry’s concept of “ready-to-recruit” populations by examining its recruitment strategies for clinical trials and the types of human subjects who participate in these drug studies. The argument is that the pharmaceutical industry has profited from a system comprised of what can more aptly be characterized as ready-to-consent populations, meaning populations who do not have better alternatives than participation in clinical trials. Further, through qualitative research, this paper aims to highlight some of the limitations of current U.S. federal regulation and to show how these limits signal problems that are not normally discussed in the medical ethics literature about research on human subjects. It does this by examining the impotence of informed consent – both as a concept and as a practice – in light of recruitment strategies and the structural reasons motivating individuals to participate in clinical trials. PMID:21359125

[Quantitative detection on contamination of Listeria monocytogenes isolated from retail ready-to-eat meats in Beijing].

PubMed

Wang, Wei; Yan, Shaofei; Bai, Li; Li, Zhigang; Du, Chunming; Li, Fengqin

2015-11-01

To survey the contamination of L. monocytogenes isolated from retail ready-to-eat meats in Beijing. Ready-to-eat meats were quantitatively detected for L. monocytogenes using MPN method. L. monocytogenes isolates were analyzed by PFGE. Fourteen out of 197 ready-to-eat meat samples were positive for L. monocytogenes with the contamination rate of 7.11% and the geometry mean contamination level of 14.31 MPN/g. The contamination of L. monocytogenes isolated from free trade market (13.89%) was more severe than those from specificity store (8.57%), supermarket (5.75%) and restaurant (2.56%), while supermarket had the highest mean contamination level of 22.78 MPN/g. A total of 13 PFGE types were characterized using DICE-UPGMA analysis through BioNumerics 7.1 software. There were two isolates from the same free trade market share the same PFGE type, which suggested the same contamination source of both samples. Contamination of L. monocytogenes exist in retail ready-to-eat meats. The contamination level of L. monocytogenes isolated from free trade market is more severe than those from specificity store, supermarket and restaurant.

SONAR: A High-Throughput Pipeline for Inferring Antibody Ontogenies from Longitudinal Sequencing of B Cell Transcripts

PubMed Central

Schramm, Chaim A.; Sheng, Zizhang; Zhang, Zhenhai; Mascola, John R.; Kwong, Peter D.; Shapiro, Lawrence

2016-01-01

The rapid advance of massively parallel or next-generation sequencing technologies has made possible the characterization of B cell receptor repertoires in ever greater detail, and these developments have triggered a proliferation of software tools for processing and annotating these data. Of especial interest, however, is the capability to track the development of specific antibody lineages across time, which remains beyond the scope of most current programs. We have previously reported on the use of techniques such as inter- and intradonor analysis and CDR3 tracing to identify transcripts related to an antibody of interest. Here, we present Software for the Ontogenic aNalysis of Antibody Repertoires (SONAR), capable of automating both general repertoire analysis and specialized techniques for investigating specific lineages. SONAR annotates next-generation sequencing data, identifies transcripts in a lineage of interest, and tracks lineage development across multiple time points. SONAR also generates figures, such as identity–divergence plots and longitudinal phylogenetic “birthday” trees, and provides interfaces to other programs such as DNAML and BEAST. SONAR can be downloaded as a ready-to-run Docker image or manually installed on a local machine. In the latter case, it can also be configured to take advantage of a high-performance computing cluster for the most computationally intensive steps, if available. In summary, this software provides a useful new tool for the processing of large next-generation sequencing datasets and the ontogenic analysis of neutralizing antibody lineages. SONAR can be found at https://github.com/scharch/SONAR, and the Docker image can be obtained from https://hub.docker.com/r/scharch/sonar/. PMID:27708645

Ni-H2 cell characterization for INTELSAT programs

NASA Technical Reports Server (NTRS)

Dunnet, Andrew F.; Earl, Martin W.

1994-01-01

Various Ni/H2 cell designs manufactured for INTELSAT Programs during the past decade have been characterized electrically as a function of temperature. The resulting data for these INTELSAT V, VI, VII and VIIA cells are assembled in a manner which allows ready comparison of performance. Also included is a detailed description of each design.

Single-Cell RNA Sequencing of Glioblastoma Cells.

PubMed

Sen, Rajeev; Dolgalev, Igor; Bayin, N Sumru; Heguy, Adriana; Tsirigos, Aris; Placantonakis, Dimitris G

2018-01-01

Single-cell RNA sequencing (sc-RNASeq) is a recently developed technique used to evaluate the transcriptome of individual cells. As opposed to conventional RNASeq in which entire populations are sequenced in bulk, sc-RNASeq can be beneficial when trying to better understand gene expression patterns in markedly heterogeneous populations of cells or when trying to identify transcriptional signatures of rare cells that may be underrepresented when using conventional bulk RNASeq. In this method, we describe the generation and analysis of cDNA libraries from single patient-derived glioblastoma cells using the C1 Fluidigm system. The protocol details the use of the C1 integrated fluidics circuit (IFC) for capturing, imaging and lysing cells; performing reverse transcription; and generating cDNA libraries that are ready for sequencing and analysis.

Efficient Skeletonization of Volumetric Objects.

PubMed

Zhou, Yong; Toga, Arthur W

1999-07-01

Skeletonization promises to become a powerful tool for compact shape description, path planning, and other applications. However, current techniques can seldom efficiently process real, complicated 3D data sets, such as MRI and CT data of human organs. In this paper, we present an efficient voxel-coding based algorithm for Skeletonization of 3D voxelized objects. The skeletons are interpreted as connected centerlines. consisting of sequences of medial points of consecutive clusters. These centerlines are initially extracted as paths of voxels, followed by medial point replacement, refinement, smoothness, and connection operations. The voxel-coding techniques have been proposed for each of these operations in a uniform and systematic fashion. In addition to preserving basic connectivity and centeredness, the algorithm is characterized by straightforward computation, no sensitivity to object boundary complexity, explicit extraction of ready-to-parameterize and branch-controlled skeletons, and efficient object hole detection. These issues are rarely discussed in traditional methods. A range of 3D medical MRI and CT data sets were used for testing the algorithm, demonstrating its utility.

Lack of glyphosate resistance gene transfer from Roundup Ready soybean to Bradyrhizobium japonicum under field and laboratory conditions.

PubMed

Isaza, Laura Arango; Opelt, Katja; Wagner, Tobias; Mattes, Elke; Bieber, Evi; Hatley, Elwood O; Roth, Greg; Sanjuán, Juan; Fischer, Hans-Martin; Sandermann, Heinrich; Hartmann, Anton; Ernst, Dieter

2011-01-01

A field study was conducted at the Russell E. Larson Agricultural Research Center to determine the effect of transgenic glyphosate-resistant soybean in combination with herbicide (Roundup) application on its endosymbiont Bradyrhizobium japonicum. DNA of bacteroids from isolated nodules was analysed for the presence of the transgenic 5-enolpyruvylshikimate-3-phosphate synthase (CP4-EPSPS) DNA sequence using polymerase chain reaction (PCR). To further assess the likelihood that the EPSPS gene may be transferred from the Roundup Ready (RR) soybean to B. japonicum, we have examined the natural transformation efficiency of B. japonicum strain 110spc4. Analyses of nodules showed the presence of the transgenic EPSPS DNA sequence. In bacteroids that were isolated from nodules of transgenic soybean plants and then cultivated in the presence of glyphosate this sequence could not be detected. This indicates that no stable horizontal gene transfer (HGT) of the EPSPS gene had occurred under field conditions. Under laboratory conditions, no natural transformation was detected in B. japonicum strain 110spc4 in the presence of various amounts of recombinant plasmid DNA. Our results indicate that no natural competence state exists in B. japonicum 110spc4. Results from field and laboratory studies indicate the lack of functional transfer of the CP4-EPSPS gene from glyphosate-tolerant soybean treated with glyphosate to root-associated B. japonicum.

National Groups Call for Big Changes in Remedial Education

ERIC Educational Resources Information Center

Mangan, Katherine

2012-01-01

Remedial courses meant to get underprepared students ready for college-level work are often not an on-ramp but a dead end, leaders of four national higher-education groups said, recommending sweeping changes in how such students are brought up to speed. Students required to take a sequence of remedial, or developmental, courses before they can…

A Directory of Selective Corrections Films.

ERIC Educational Resources Information Center

Lankes, George A.

This directory of selective film titles has been prepared to serve as a ready index to many of the films of potential value for the enrichment of a corrections curriculum. Recognizing that the list is not complete, the directory has been assembled in a manner which allows for adding titles by alphabetic sequence on the blank sides of the pages.…

Linking household and health facility surveys to assess obstetric service availability, readiness and coverage: evidence from 17 low- and middle-income countries.

PubMed

Kanyangarara, Mufaro; Chou, Victoria B; Creanga, Andreea A; Walker, Neff

2018-06-01

Improving access and quality of obstetric service has the potential to avert preventable maternal, neonatal and stillborn deaths, yet little is known about the quality of care received. This study sought to assess obstetric service availability, readiness and coverage within and between 17 low- and middle-income countries. We linked health facility data from the Service Provision Assessments and Service Availability and Readiness Assessments, with corresponding household survey data obtained from the Demographic and Health Surveys and Multiple Indicator Cluster Surveys. Based on performance of obstetric signal functions, we defined four levels of facility emergency obstetric care (EmOC) functionality: comprehensive (CEmOC), basic (BEmOC), BEmOC-2, and low/substandard. Facility readiness was evaluated based on the direct observation of 23 essential items; facilities "ready to provide obstetric services" had ≥20 of 23 items available. Across countries, we used medians to characterize service availability and readiness, overall and by urban-rural location; analyses also adjusted for care-seeking patterns to estimate population-level coverage of obstetric services. Of the 111 500 health facilities surveyed, 7545 offered obstetric services and were included in the analysis. The median percentages of facilities offering EmOC and "ready to provide obstetric services" were 19% and 10%, respectively. There were considerable urban-rural differences, with absolute differences of 19% and 29% in the availability of facilities offering EmOC and "ready to provide obstetric services", respectively. Adjusting for care-seeking patterns, results from the linking approach indicated that among women delivering in a facility, a median of 40% delivered in facilities offering EmOC, and 28% delivered in facilities "ready to provide obstetric services". Relatively higher coverage of facility deliveries (≥65%) and coverage of deliveries in facilities "ready to provide obstetric services" (≥30% of facility deliveries) were only found in three countries. The low levels of availability, readiness and coverage of obstetric services documented represent substantial missed opportunities within health systems. Global and national efforts need to prioritize upgrading EmOC functionality and improving readiness to deliver obstetric service, particularly in rural areas. The approach of linking health facility and household surveys described here could facilitate the tracking of progress towards quality obstetric care.

Linking household and health facility surveys to assess obstetric service availability, readiness and coverage: evidence from 17 low- and middle-income countries

PubMed Central

Kanyangarara, Mufaro; Chou, Victoria B; Creanga, Andreea A; Walker, Neff

2018-01-01

Background Improving access and quality of obstetric service has the potential to avert preventable maternal, neonatal and stillborn deaths, yet little is known about the quality of care received. This study sought to assess obstetric service availability, readiness and coverage within and between 17 low- and middle-income countries. Methods We linked health facility data from the Service Provision Assessments and Service Availability and Readiness Assessments, with corresponding household survey data obtained from the Demographic and Health Surveys and Multiple Indicator Cluster Surveys. Based on performance of obstetric signal functions, we defined four levels of facility emergency obstetric care (EmOC) functionality: comprehensive (CEmOC), basic (BEmOC), BEmOC-2, and low/substandard. Facility readiness was evaluated based on the direct observation of 23 essential items; facilities “ready to provide obstetric services” had ≥20 of 23 items available. Across countries, we used medians to characterize service availability and readiness, overall and by urban-rural location; analyses also adjusted for care-seeking patterns to estimate population-level coverage of obstetric services. Results Of the 111 500 health facilities surveyed, 7545 offered obstetric services and were included in the analysis. The median percentages of facilities offering EmOC and “ready to provide obstetric services” were 19% and 10%, respectively. There were considerable urban-rural differences, with absolute differences of 19% and 29% in the availability of facilities offering EmOC and “ready to provide obstetric services”, respectively. Adjusting for care-seeking patterns, results from the linking approach indicated that among women delivering in a facility, a median of 40% delivered in facilities offering EmOC, and 28% delivered in facilities “ready to provide obstetric services”. Relatively higher coverage of facility deliveries (≥65%) and coverage of deliveries in facilities “ready to provide obstetric services” (≥30% of facility deliveries) were only found in three countries. Conclusions The low levels of availability, readiness and coverage of obstetric services documented represent substantial missed opportunities within health systems. Global and national efforts need to prioritize upgrading EmOC functionality and improving readiness to deliver obstetric service, particularly in rural areas. The approach of linking health facility and household surveys described here could facilitate the tracking of progress towards quality obstetric care. PMID:29862026

HPV-QUEST: A highly customized system for automated HPV sequence analysis capable of processing Next Generation sequencing data set.

PubMed

Yin, Li; Yao, Jiqiang; Gardner, Brent P; Chang, Kaifen; Yu, Fahong; Goodenow, Maureen M

2012-01-01

Next Generation sequencing (NGS) applied to human papilloma viruses (HPV) can provide sensitive methods to investigate the molecular epidemiology of multiple type HPV infection. Currently a genotyping system with a comprehensive collection of updated HPV reference sequences and a capacity to handle NGS data sets is lacking. HPV-QUEST was developed as an automated and rapid HPV genotyping system. The web-based HPV-QUEST subtyping algorithm was developed using HTML, PHP, Perl scripting language, and MYSQL as the database backend. HPV-QUEST includes a database of annotated HPV reference sequences with updated nomenclature covering 5 genuses, 14 species and 150 mucosal and cutaneous types to genotype blasted query sequences. HPV-QUEST processes up to 10 megabases of sequences within 1 to 2 minutes. Results are reported in html, text and excel formats and display e-value, blast score, and local and coverage identities; provide genus, species, type, infection site and risk for the best matched reference HPV sequence; and produce results ready for additional analyses.

Process development for automated solar cell and module production. Task 4: Automated array assembly

NASA Technical Reports Server (NTRS)

1980-01-01

A process sequence which can be used in conjunction with automated equipment for the mass production of solar cell modules for terrestrial use was developed. The process sequence was then critically analyzed from a technical and economic standpoint to determine the technological readiness of certain process steps for implementation. The steps receiving analysis were: back contact metallization, automated cell array layup/interconnect, and module edge sealing. For automated layup/interconnect, both hard automation and programmable automation (using an industrial robot) were studied. The programmable automation system was then selected for actual hardware development.

A Module Experimental Process System Development Unit (MEPSDU)

NASA Technical Reports Server (NTRS)

1981-01-01

The purpose of this program is to demonstrate the technical readiness of a cost effective process sequence that has the potential for the production of flat plate photovoltaic modules which met the price goal in 1986 of $.70 or less per watt peak. Program efforts included: preliminary design review, preliminary cell fabrication using the proposed process sequence, verification of sandblasting back cleanup, study of resist parameters, evaluation of pull strength of the proposed metallization, measurement of contact resistance of Electroless Ni contacts, optimization of process parameter, design of the MEPSDU module, identification and testing of insulator tapes, development of a lamination process sequence, identification, discussions, demonstrations and visits with candidate equipment vendors, evaluation of proposals for tabbing and stringing machine.

The Effects of Mandated Career and Technical Education (CTE) on the College and Career Preparation of High School Students

ERIC Educational Resources Information Center

Hagen, Stephen N.

2010-01-01

College and career readiness offers a distinct purpose to the high school experience. This experience must provide a variety of options with a clear focus on fruitful opportunities for success. Meaningful citizenship in any learning community demands that all students participate in a pathway of sequenced, practical, related classes and achieve…

Large area, low cost solar cell development and production readiness

NASA Technical Reports Server (NTRS)

Michaels, D.

1982-01-01

A process sequence for a large area ( or = 25 sq. cm) silicon solar cell was investigated. Generic cell choice was guided by the expected electron fluence, by the packing factors of various cell envelope designs onto each panel to provide needed voltage as well as current, by the weight constraints on the system, and by the cost goals of the contract.

Applying the Transtheoretical Model of Change to the Sequencing of Ethics Instruction in Business Education

ERIC Educational Resources Information Center

Tyler, Catherine L.; Tyler, J. Michael

2006-01-01

Although there is widespread agreement on the importance of ethics instruction in business education, there is not agreement on the best approach or timing of instruction. This article uses J. O. Prochaska and DiClemente's transtheoretical model of change as the basis for a developmental model of student readiness for learning about ethics. By…

College Readiness as a Graduation Requirement: An Assessment of San Diego's Challenges

ERIC Educational Resources Information Center

Betts, Julian R.; Zau, Andrew C.; Bachofer, Karen Volz

2013-01-01

To be considered for admission to the University of California (UC) or the California State University (CSU) system, high school students must complete all a-g courses with grades of C or higher. The a-g course sequence includes 30 semesters of UC-approved college preparatory coursework in seven subject areas, and completion indicates a high level…

Exploring Writing Workshop in the K-2 Classroom: Discovering Our Voices. Bill Harp Professional Teachers Library Series.

ERIC Educational Resources Information Center

Rickards, Debbie; Hawes, Shirl

This book is meant as a resource that can be used by experienced writing teachers as a practical reference when planning writing lessons. The book includes a sequence of instruction, lesson ideas, enrichment options, literature and poetry connections, student samples, and all the ready-to-use materials teachers need to implement the…

Development of a peptide nucleic acid polymerase chain reaction clamping assay for semiquantitative evaluation of genetically modified organism content in food.

PubMed

Peano, C; Lesignoli, F; Gulli, M; Corradini, R; Samson, M C; Marchelli, R; Marmiroli, N

2005-09-15

In the present study a peptide nucleic acid (PNA)-mediated polymerase chain reaction (PCR) clamping method was developed and applied to the detection of genetically modified organisms (GMO), to test PCR products for band identity and to obtain a semiquantitative evaluation of GMO content. The minimal concentration of PNA necessary to block the PCR was determined by comparing PCRs containing a constant amount of DNA in the presence of increasing concentration of target-specific PNA. The lowest PNA concentration at which specific inhibition took place, by the inhibition of primer extension and/or steric hindrance, was the most efficient condition. Optimization of PCR clamping by PNA was observed by testing five different PNAs with a minimum of 13 bp to a maximum of 15 bp, designed on the target sequence of Roundup Ready soybean. The results obtained on the DNA extracted from Roundup Ready soybean standard flour were verified also on DNA extracted from standard flours of maize GA21, Bt176, Bt11, and MON810. A correlation between the PNA concentration necessary for inducing PCR clamping and the percentage of the GMO target sequence in the sample was found.

Serving high-risk foods in a high-risk setting: survey of hospital food service practices after an outbreak of listeriosis in a hospital.

PubMed

Cokes, Carolyn; France, Anne Marie; Reddy, Vasudha; Hanson, Heather; Lee, Lillian; Kornstein, Laura; Stavinsky, Faina; Balter, Sharon

2011-04-01

Prepared ready-to-eat salads and ready-to-eat delicatessen-style meats present a high risk for Listeria contamination. Because no foodborne illness risk management guidelines exist specifically for US hospitals, a survey of New York City (NYC) hospitals was conducted to characterize policies and practices after a listeriosis outbreak occurred in a NYC hospital. From August through October 2008, a listeriosis outbreak in a NYC hospital was investigated. From February through April 2009, NYC's 61 acute-care hospitals were asked to participate in a telephone survey regarding food safety practices and policies, specifically service of high-risk foods to patients at increased risk for listeriosis. Five patients with medical conditions that put them at high risk for listeriosis had laboratory-confirmed Listeria monocytogenes infection. The Listeria outbreak strain was isolated from tuna salad prepared in the hospital. Fifty-four (89%) of 61 hospitals responded to the survey. Overall, 81% of respondents reported serving ready-to-eat deli meats to patients, and 100% reported serving prepared ready-to-eat salads. Pregnant women, patients receiving immunosuppressive drugs, and patients undergoing chemotherapy were served ready-to-eat deli meats at 77%, 59%, and 49% of hospitals, respectively, and were served prepared ready-to-eat salads at 94%, 89%, and 73% of hospitals, respectively. Only 4 (25%) of 16 respondents reported having a policy that ready-to-eat deli meats must be heated until steaming hot before serving. Despite the potential for severe outcomes of Listeria infection among hospitalized patients, the majority of NYC hospitals had no food preparation policies to minimize risk. Hospitals should implement policies to avoid serving high-risk foods to patients at risk for listeriosis.

DURIP: An Ultrafast Testbed for Comprehensive Characterization of Photonics, Electronic, and Optoelectronic Properties of Inegrated Nanophotonic Structures

DTIC Science & Technology

2017-10-14

Department of the Army position, policy or decision , unless so designated by other documentation. 9. SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS (ES...characterization equipment to an al- ready available photonic characterization setup. The following table details of the spent budget and the list of purchased ...measure the response of a high-speed optical signal processing platform. The same architecture also can be used to charac- terize high-speed

Investigating Student Understanding for a Statistical Analysis of Two Thermally Interacting Solids

NASA Astrophysics Data System (ADS)

Loverude, Michael E.

2010-10-01

As part of an ongoing research and curriculum development project for upper-division courses in thermal physics, we have developed a sequence of tutorials in which students apply statistical methods to examine the behavior of two interacting Einstein solids. In the sequence, students begin with simple results from probability and develop a means for counting the states in a single Einstein solid. The students then consider the thermal interaction of two solids, and observe that the classical equilibrium state corresponds to the most probable distribution of energy between the two solids. As part of the development of the tutorial sequence, we have developed several assessment questions to probe student understanding of various aspects of this system. In this paper, we describe the strengths and weaknesses of student reasoning, both qualitative and quantitative, to assess the readiness of students for one tutorial in the sequence.

Whole-genome Sequencing Used to Investigate a Nationwide Outbreak of Listeriosis Caused by Ready-to-eat Delicatessen Meat, Denmark, 2014.

PubMed

Kvistholm Jensen, Anne; Nielsen, Eva Møller; Björkman, Jonas Torgny; Jensen, Tenna; Müller, Luise; Persson, Søren; Bjerager, Gitte; Perge, Annette; Krause, Tyra Grove; Kiil, Kristoffer; Sørensen, Gitte; Andersen, Jens Kirk; Mølbak, Kåre; Ethelberg, Steen

2016-07-01

Listeriosis is a serious foodborne infection. Outbreaks of listeriosis occur rarely, but have often proved difficult to solve. In June 2014, we detected and investigated a listeriosis outbreak in Denmark using patient interviews and whole-genome sequencing (WGS). We performed WGS on Listeria monocytogenes isolates from patients and available isolates from ready-to-eat foods and compared them using single-nucleotide polymorphism (SNP) analysis. Case patients had L. monocytogenes with ≤3 SNPs (the outbreak strain) isolated in September 2013-December 2014. Through interviews, we established case patients' food and clinical histories. Food production facilities were inspected and sampled, and we performed trace-back/trace-forward of food delivery chains. In total, 41 cases were identified; 17 deaths occurred (41%). An isolate from a delicatessen meat (spiced meat roll) from company A was identical to the outbreak strain. Half of the patients were infected while hospitalized/institutionalized; institutions were supplied food by company A. The outbreak strain was repeatedly isolated from further samples taken within this company and within companies in its distribution chain. Products from company A were traced and recalled from >6000 food establishments, after which the outbreak ended. Ready-to-eat spiced meat roll from a single production facility caused this outbreak. The product, served sliced and cold, is popular among the elderly; serving it at hospitals probably contributed to the high case-fatality rate. WGS used for patient isolates and isolates from food control inspections, coupled with routine epidemiological follow-up, was instrumental in swiftly locating the source of infections, preventing further illnesses and deaths. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

A Module Experimental Process System Development Unit (MEPSDU). [development of low cost solar arrays

NASA Technical Reports Server (NTRS)

1981-01-01

The technical readiness of a cost effective process sequence that has the potential for the production of flat plate photovoltaic modules which met the price goal in 1986 of $.70 or less per Watt peak was demonstrated. The proposed process sequence was reviewed and laboratory verification experiments were conducted. The preliminary process includes the following features: semicrystalline silicon (10 cm by 10 cm) as the silicon input material; spray on dopant diffusion source; Al paste BSF formation; spray on AR coating; electroless Ni plate solder dip metallization; laser scribe edges; K & S tabbing and stringing machine; and laminated EVA modules.

Improvements and modifications to the NASA microwave signature acquisition system

NASA Technical Reports Server (NTRS)

Jean, B. R.; Newton, R. W.; Warren, G. L.; Clark, B. V.; Zajicek, J. L.

1978-01-01

A user oriented description of the modified and upgraded Microwave Signature Acquisition System is provided. The present configuration of the sensor system and its operating characteristics are documented and a step-by-step operating procedure provides instruction for mounting the antenna truss assembly, readying the system for data acquisition, and for controlling the system during the data collection sequence. The resulting data products are also identified.

Phase 1 of the automated array assembly task of the low cost silicon solar array project

NASA Technical Reports Server (NTRS)

Coleman, M. G.; Pryor, R. A.; Grenon, L. A.; Lesk, I. A.

1977-01-01

The state of technology readiness for the automated production of solar cells and modules is reviewed. Individual process steps and process sequences for making solar cells and modules were evaluated both technically and economically. High efficiency with a suggested cell goal of 15% was stressed. It is concluded that the technology exists to manufacture solar cells which will meet program goals.

Low cost solar array project production process and equipment task. A Module Experimental Process System Development Unit (MEPSDU)

NASA Technical Reports Server (NTRS)

1981-01-01

Technical readiness for the production of photovoltaic modules using single crystal silicon dendritic web sheet material is demonstrated by: (1) selection, design and implementation of solar cell and photovoltaic module process sequence in a Module Experimental Process System Development Unit; (2) demonstration runs; (3) passing of acceptance and qualification tests; and (4) achievement of a cost effective module.

The Importance of Being Playful.

ERIC Educational Resources Information Center

Bodrova, Elena; Leong, Deborah J.

2003-01-01

Recent research provides evidence of the strong connections between quality of play in preschool years and children's readiness for school instruction. Mature play, characterized by imaginary situations, multiple roles, clearly defined rules, flexible themes, language development, length of play, helps students' cognitive development. (Contains 12…

A Proteomic Workflow Using High-Throughput De Novo Sequencing Towards Complementation of Genome Information for Improved Comparative Crop Science.

PubMed

Turetschek, Reinhard; Lyon, David; Desalegn, Getinet; Kaul, Hans-Peter; Wienkoop, Stefanie

2016-01-01

The proteomic study of non-model organisms, such as many crop plants, is challenging due to the lack of comprehensive genome information. Changing environmental conditions require the study and selection of adapted cultivars. Mutations, inherent to cultivars, hamper protein identification and thus considerably complicate the qualitative and quantitative comparison in large-scale systems biology approaches. With this workflow, cultivar-specific mutations are detected from high-throughput comparative MS analyses, by extracting sequence polymorphisms with de novo sequencing. Stringent criteria are suggested to filter for confidential mutations. Subsequently, these polymorphisms complement the initially used database, which is ready to use with any preferred database search algorithm. In our example, we thereby identified 26 specific mutations in two cultivars of Pisum sativum and achieved an increased number (17 %) of peptide spectrum matches.

Characterization of environmental cues for initiation of reproductive cycling and spawning in shovelnose sturgeon Scaphirhynchus platorynchus in the Lower Missouri River, USA

USGS Publications Warehouse

Papoulias, D.M.; DeLonay, A.J.; Annis, M.L.; Wildhaber, M.L.; Tillitt, D.E.

2011-01-01

We presume that the shovelnose sturgeon (Scaphirhynchus platorynchus) has evolved to spawn in the springtime when environmental conditions are at some optimum, but this state has not yet been defined. In this study physiological readiness to spawn in shovelnose sturgeon was examined to define more closely when spawning could occur and thus identify and evaluate prevailing environmental conditions that could cue spawning during that period. Reproductive assessments of Lower Missouri River shovelnose during 4 years (2005-2008) and at two locations (Gavins Point Dam, South Dakota and Boonville, Missouri) were used to identify shovelnose sturgeon spawning periods. Initiation of the spawning period, as defined by the presence of reproductively ready fish, was a highly predictable yearly event and extended over several weeks at each reach. The spawning period occurred earlier in the lower reach than in the upper reach and environmental conditions during the periods varied between locations and among years. Shovelnose sturgeon collected during the presumed spawning periods were at varying degrees of readiness to spawn as indicated by oocyte polarization index and blood reproductive hormones. Evaluation of the influence of environmental factors on readiness to spawn using stepwise multiple regression analysis indicated photoperiod followed by temperature were the best candidate variables overall to explain the trend. However, within geographically distinct populations gravid females are not all reproductively synchronized. Assuming that this apparent asynchrony in readiness is normal and not an artifact of the disturbed Missouri River system, we infer that individual sturgeon can persist in a reproductively ready state until conditions appropriate for spawning occur. Taken together, our results lead us to hypothesize that gravid females early in the reproductive cycle (post-vitellogenesis) respond to day length, a reliable annual cue, become increasingly more ready to spawn in response to temperature, and that another set of cues, short-term and specific for localized environmental conditions or events, serve to signal ovulation and release of gametes.

Neighbourhood ethnic diversity buffers school readiness impact in ESL children.

PubMed

Puchala, Chassidy; Vu, Lan T H; Muhajarine, Nazeem

2010-01-01

Contextual factors, as measured by neighbourhood characteristics, shape the experiences children have and affect their "school readiness", i.e., whether they are well or poorly prepared for the transition from home to kindergarten. This study assessed the independent effects of individual and neighbourhood factors on school readiness; specifically, it examined whether and to what degree neighbourhood factors modified children's language ability and thus their school readiness in a population of children in Saskatoon, Saskatchewan. The study included all children attending kindergarten in 2001, 2003 and 2005 in Saskatoon. School readiness and child characteristics were measured by the Early Development Instrument (EDI). The EDI measures child development at school commencement in five domains: physical health and well-being, social competence, emotional maturity, cognitive and language development, and communication skills and general knowledge. Data from the 2001 Census were used to characterize Saskatoon's neighbourhoods. Multilevel modeling examined the independent and buffering or exacerbating effects of individual and neighbourhood factors on the relation between English as a Second Language (ESL) status in children and EDI domain scores. ESL children had significantly lower scores on all EDI domains compared with non-ESL children. Certain factors (e.g., younger age, male, Aboriginal status, having special needs) were significantly related to lower readiness in terms of the emotional maturity, and communication skills and general knowledge domains. Importantly, children who lived in neighbourhoods that were highly transient (with a higher proportion of residents who had moved in the previous year) had lower EDI scores on both domains, and those in neighbourhoods with lower rates of employment had lower EDI scores on communication skills and general knowledge. Neighbourhood ethnic diversity mitigated the negative impact of ESL status on school readiness for both domains. ESL children from neighbourhoods with a high degree of ethnic diversity had higher EDI scores than ESL children from neighbourhoods with low ethnic diversity. The current study provided insight regarding the impact of contextual factors in addition to individual factors, such as ESL status, on school readiness outcomes. Future research should continue to examine contextual factors related to ESL status and early child developmental outcomes, particularly focusing on the mechanisms of influence.

Surface Imprints: Advantageous Application of Ready2use Materials for Bacterial Quartz-Crystal Microbalance Sensors.

PubMed

Poller, Anna-Maria; Spieker, Eva; Lieberzeit, Peter A; Preininger, Claudia

2017-01-11

Four different materials (two ab initio synthesized polyurethanes; ready-to-use: Epon1002F and poly(vinyl alcohol)/N-methyl-4(4'-formylstyryl)pyridinium methosulfate acetal) for the generation of Escherichia coli surface imprints are compared in this work. The use of commercially available, ready-to-use materials instead of self-synthesized polymers represents an innovative and convenient way of molecular imprint fabrication. This was herein investigated for large, biological templates. Fully synthesized imprint materials (polyurethanes) were developed and optimized regarding their OH excess and the use of catalyst in the polymerization reaction. No to low OH excess (0-10%) and a noncatalyzed synthesis were determined to be superior for the imprinting of the Gram-negative bacteria. Imprints were characterized using atomic force microscopy, with Epon1002F yielding the most distinguished imprints, along with a smooth surface. The imprints were afterward tested as plastic antibody coatings in a mass-sensitive quartz-crystal microbalance measurement. Dilutions of E. coli suspensions, down to a limit of detection of 1.4 × 10 7 CFU/mL, were successfully measured. Best results were obtained with Epon1002F and self-synthesized, stoichiometric polyurethane. Since ready-to-use Epon1002F was superior in terms of signal intensities and sensitivity, it can advantageously replace self-synthesized polymers for the generation of imprinted sensor surfaces. Easy day-to-day reproducibility and further shortening of imprint fabrication time are other advantages of employing the ready-to-use material instead of conventionally synthesized polymers.

Using Dynamic Assessment to Evaluate the Expressive Syntax of Children who use Augmentative and Alternative Communication

PubMed Central

King, Marika R.; Binger, Cathy; Kent-Walsh, Jennifer

2015-01-01

The developmental readiness of four 5-year-old children to produce basic sentences using graphic symbols on an augmentative and alternative communication (AAC) device during a dynamic assessment (DA) task was examined. Additionally, the ability of the DA task to predict performance on a subsequent experimental task was evaluated. A graduated prompting framework was used during DA. Measures included amount of support required to produce the targets, modifiability (change in participant performance) within a DA session, and predictive validity of DA. Participants accurately produced target structures with varying amounts of support. Modifiability within DA sessions was evident for some participants, and partial support was provided for the measures of predictive validity. These initial results indicate that DA may be a viable way to measure young children’s developmental readiness to learn how to sequence simple, rule-based messages via aided AAC. PMID:25621928

Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations

PubMed Central

Marinier, Eric; Zaheer, Rahat; Berry, Chrystal; Weedmark, Kelly A.; Domaratzki, Michael; Mabon, Philip; Knox, Natalie C.; Reimer, Aleisha R.; Graham, Morag R.; Chui, Linda; Patterson-Fortin, Laura; Zhang, Jian; Pagotto, Franco; Farber, Jeff; Mahony, Jim; Seyer, Karine; Bekal, Sadjia; Tremblay, Cécile; Isaac-Renton, Judy; Prystajecky, Natalie; Chen, Jessica; Slade, Peter

2017-01-01

Abstract The ready availability of vast amounts of genomic sequence data has created the need to rethink comparative genomics algorithms using ‘big data’ approaches. Neptune is an efficient system for rapidly locating differentially abundant genomic content in bacterial populations using an exact k-mer matching strategy, while accommodating k-mer mismatches. Neptune’s loci discovery process identifies sequences that are sufficiently common to a group of target sequences and sufficiently absent from non-targets using probabilistic models. Neptune uses parallel computing to efficiently identify and extract these loci from draft genome assemblies without requiring multiple sequence alignments or other computationally expensive comparative sequence analyses. Tests on simulated and real datasets showed that Neptune rapidly identifies regions that are both sensitive and specific. We demonstrate that this system can identify trait-specific loci from different bacterial lineages. Neptune is broadly applicable for comparative bacterial analyses, yet will particularly benefit pathogenomic applications, owing to efficient and sensitive discovery of differentially abundant genomic loci. The software is available for download at: http://github.com/phac-nml/neptune. PMID:29048594

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases.

PubMed

Shen, Li; Shao, Ningyi; Liu, Xiaochuan; Nestler, Eric

2014-04-15

Understanding the relationship between the millions of functional DNA elements and their protein regulators, and how they work in conjunction to manifest diverse phenotypes, is key to advancing our understanding of the mammalian genome. Next-generation sequencing technology is now used widely to probe these protein-DNA interactions and to profile gene expression at a genome-wide scale. As the cost of DNA sequencing continues to fall, the interpretation of the ever increasing amount of data generated represents a considerable challenge. We have developed ngs.plot - a standalone program to visualize enrichment patterns of DNA-interacting proteins at functionally important regions based on next-generation sequencing data. We demonstrate that ngs.plot is not only efficient but also scalable. We use a few examples to demonstrate that ngs.plot is easy to use and yet very powerful to generate figures that are publication ready. We conclude that ngs.plot is a useful tool to help fill the gap between massive datasets and genomic information in this era of big sequencing data.

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

PubMed Central

2014-01-01

Background Understanding the relationship between the millions of functional DNA elements and their protein regulators, and how they work in conjunction to manifest diverse phenotypes, is key to advancing our understanding of the mammalian genome. Next-generation sequencing technology is now used widely to probe these protein-DNA interactions and to profile gene expression at a genome-wide scale. As the cost of DNA sequencing continues to fall, the interpretation of the ever increasing amount of data generated represents a considerable challenge. Results We have developed ngs.plot – a standalone program to visualize enrichment patterns of DNA-interacting proteins at functionally important regions based on next-generation sequencing data. We demonstrate that ngs.plot is not only efficient but also scalable. We use a few examples to demonstrate that ngs.plot is easy to use and yet very powerful to generate figures that are publication ready. Conclusions We conclude that ngs.plot is a useful tool to help fill the gap between massive datasets and genomic information in this era of big sequencing data. PMID:24735413

Assessing Organizational Readiness for a Participatory Occupational Health/Health Promotion Intervention in Skilled Nursing Facilities

PubMed Central

Zhang, Yuan; Flum, Marian; West, Cheryl; Punnett, Laura

2018-01-01

The long-term care sector is characterized by high morbidity and employee turnover, along with associated costs. Effective health protection and health promotion are important to improve physical and psychosocial well-being of caregivers. Assessment of organizational readiness for change is an essential precursor to the successful implementation of workplace programs addressing work climate, structure of tasks and relationships, and other issues that may be perceived as challenging by some within the institution. This study qualitatively assessed readiness of five skilled nursing facilities for a participatory occupational health/health promotion intervention. Selection criteria were developed to screen for program feasibility and ability to conduct prospective evaluations, and information was collected from managers and employees (interviews and focus groups). Three centers were selected for the program, and the first year of formative evaluation and intervention experience was then reviewed to evaluate and modify our selection criteria after the fact. Lessons learned include adding assessment of communication and the structure of problem solving to our selection criteria, improving methods to assess management support in a concrete (potentially nonverbal) form, and obtaining a stated financial commitment and resources to enable the team to function. Assessment of organizational readiness for change is challenging, although necessary to implement effective and sustainable health promotion programs in specific organizations. PMID:25715335

Optimization of Biofuel Production from Transgenic Microalgae

DTIC Science & Technology

2008-05-31

are ready to transform. We are nearing completion of a Rubisco construct linked to carbonic anhydrase to increase the C02 concentration near the active...site of Rubisco to inhibit photorespiration. In addition, we have started a project on characterizing the proteomes of cells induced to produce

Sensory characterization of a ready-to-eat sweetpotato breakfast cereal by descriptive analysis

NASA Technical Reports Server (NTRS)

Dansby, M. A.; Bovell-Benjamin, A. C.

2003-01-01

The sweetpotato [Ipomoea batatas (L.) Lam], an important industry in the United States, has been selected as a candidate crop to be grown on future long-duration space missions by NASA. Raw sweetpotato roots were processed into flour, which was used to formulate ready-to-eat breakfast cereal (RTEBC). Twelve trained panelists evaluated the sensory attributes of the extruded RTEBC using descriptive analysis. The samples were significantly different (P<0.05) for all attributes. Twelve perceived sensory attributes, which could be used to differentiate the appearance, texture, and flavor of sweetpotato RTEBC, were described. The data could be used to optimize the RTEBC and for designing studies to test its consumer acceptance.

Genome Wide Characterization of Simple Sequence Repeats in Cucumber

USDA-ARS?s Scientific Manuscript database

The whole genome sequence of the cucumber cultivar Gy14 was recently sequenced at 15× coverage with the Roche 454 Titanium technology. The microsatellite DNA sequences (simple sequence repeats, SSRs) in the assembled scaffolds were computationally explored and characterized. A total of 112,073 SSRs ...

Genomic Epidemiology of Tuberculosis.

PubMed

Comas, Iñaki

2017-01-01

The application of next generation sequencing technologies has opened the door to a new molecular epidemiology of tuberculosis, in which we can now look at transmission at a resolution not possible before. At the same time, new technical and analytical challenges have appeared, and we are still exploring the wider potential of this new technology. Whole genome sequencing in tuberculosis still requires bacterial cultures. Thus, although whole genome sequencing has revolutionized the interpretation of transmission patterns, it is not yet ready to be applied at the point-of-care. In this chapter, I will review the promises and challenges of genomic epidemiology, as well as some of the new questions that have arisen from the use of this new technology. In addition, I will examine the role of molecular epidemiology within the general frame of global tuberculosis control and how genomic epidemiology can contribute towards the elimination of the disease.

National outbreak of Salmonella Give linked to a local food manufacturer in Malta, October 2016.

PubMed

Donachie, A; Melillo, T; Bubba, L; Hartman, H; Borg, M-L

2018-06-26

Salmonella Give is a rare serotype across Europe. In October 2016, a national outbreak of S. Give occurred in Malta. We describe the epidemiological, environmental, microbiological and veterinary investigations. Whole-genome sequencing (WGS) was performed on human, food, environmental and veterinary isolates. Thirty-six human cases were reported between October and November 2016, 10 (28%) of whom required hospitalisation. Twenty-six (72%) cases were linked to four restaurants. S. Give was isolated from ready-to-eat antipasti served by three restaurants which were all supplied by the same local food manufacturer. Food-trace-back investigations identified S. Give in packaged bean dips, ham, pork and an asymptomatic food handler at the manufacturer; inspections found inadequate separation between raw and ready-to-eat food during processing. WGS indicated two genetically distinguishable strains of S. Give with two distinct clusters identified; one cluster linked to the local food manufacturer and a second linked to veterinary samples. Epidemiological, environmental and WGS evidence pointed towards cross-contamination of raw and ready-to-eat foods at the local manufacturer as the likely source of one cluster. Severity of illness indicates a high virulence of this specific serotype. To prevent future cases and outbreaks, adherence to food safety practices at manufacturing level need to be reinforced.

Comparing Emission Inventories and Model-Ready Emission Datasets between Europe and North America for the AQMEII Project

EPA Science Inventory

This paper highlights the similarities and differences in how emission inventories and datasets were developed and processed across North America and Europe for the Air Quality Model Evaluation International Initiative (AQMEII) project and then characterizes the emissions for the...

Targeted amplicon sequencing (TAS): a scalable next-gen approach to multilocus, multitaxa phylogenetics.

PubMed

Bybee, Seth M; Bracken-Grissom, Heather; Haynes, Benjamin D; Hermansen, Russell A; Byers, Robert L; Clement, Mark J; Udall, Joshua A; Wilcox, Edward R; Crandall, Keith A

2011-01-01

Next-gen sequencing technologies have revolutionized data collection in genetic studies and advanced genome biology to novel frontiers. However, to date, next-gen technologies have been used principally for whole genome sequencing and transcriptome sequencing. Yet many questions in population genetics and systematics rely on sequencing specific genes of known function or diversity levels. Here, we describe a targeted amplicon sequencing (TAS) approach capitalizing on next-gen capacity to sequence large numbers of targeted gene regions from a large number of samples. Our TAS approach is easily scalable, simple in execution, neither time-nor labor-intensive, relatively inexpensive, and can be applied to a broad diversity of organisms and/or genes. Our TAS approach includes a bioinformatic application, BarcodeCrucher, to take raw next-gen sequence reads and perform quality control checks and convert the data into FASTA format organized by gene and sample, ready for phylogenetic analyses. We demonstrate our approach by sequencing targeted genes of known phylogenetic utility to estimate a phylogeny for the Pancrustacea. We generated data from 44 taxa using 68 different 10-bp multiplexing identifiers. The overall quality of data produced was robust and was informative for phylogeny estimation. The potential for this method to produce copious amounts of data from a single 454 plate (e.g., 325 taxa for 24 loci) significantly reduces sequencing expenses incurred from traditional Sanger sequencing. We further discuss the advantages and disadvantages of this method, while offering suggestions to enhance the approach.

Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics

PubMed Central

Bybee, Seth M.; Bracken-Grissom, Heather; Haynes, Benjamin D.; Hermansen, Russell A.; Byers, Robert L.; Clement, Mark J.; Udall, Joshua A.; Wilcox, Edward R.; Crandall, Keith A.

2011-01-01

Next-gen sequencing technologies have revolutionized data collection in genetic studies and advanced genome biology to novel frontiers. However, to date, next-gen technologies have been used principally for whole genome sequencing and transcriptome sequencing. Yet many questions in population genetics and systematics rely on sequencing specific genes of known function or diversity levels. Here, we describe a targeted amplicon sequencing (TAS) approach capitalizing on next-gen capacity to sequence large numbers of targeted gene regions from a large number of samples. Our TAS approach is easily scalable, simple in execution, neither time-nor labor-intensive, relatively inexpensive, and can be applied to a broad diversity of organisms and/or genes. Our TAS approach includes a bioinformatic application, BarcodeCrucher, to take raw next-gen sequence reads and perform quality control checks and convert the data into FASTA format organized by gene and sample, ready for phylogenetic analyses. We demonstrate our approach by sequencing targeted genes of known phylogenetic utility to estimate a phylogeny for the Pancrustacea. We generated data from 44 taxa using 68 different 10-bp multiplexing identifiers. The overall quality of data produced was robust and was informative for phylogeny estimation. The potential for this method to produce copious amounts of data from a single 454 plate (e.g., 325 taxa for 24 loci) significantly reduces sequencing expenses incurred from traditional Sanger sequencing. We further discuss the advantages and disadvantages of this method, while offering suggestions to enhance the approach. PMID:22002916

Automated landmarking and geometric characterization of the carotid siphon.

PubMed

Bogunović, Hrvoje; Pozo, José María; Cárdenes, Rubén; Villa-Uriol, María Cruz; Blanc, Raphaël; Piotin, Michel; Frangi, Alejandro F

2012-05-01

The geometry of the carotid siphon has a large variability between subjects, which has prompted its study as a potential geometric risk factor for the onset of vascular pathologies on and off the internal carotid artery (ICA). In this work, we present a methodology for an objective and extensive geometric characterization of carotid siphon parameterized by a set of anatomical landmarks. We introduce a complete and automated characterization pipeline. Starting from the segmentation of vasculature from angiographic image and its centerline extraction, we first identify ICA by characterizing vessel tree bifurcations and training a support vector machine classifier to detect ICA terminal bifurcation. On ICA centerline curve, we detect anatomical landmarks of carotid siphon by modeling it as a sequence of four bends and selecting their centers and interfaces between them. Bends are detected from the trajectory of the curvature vector expressed in the parallel transport frame of the curve. Finally, using the detected landmarks, we characterize the geometry in two complementary ways. First, with a set of local and global geometric features, known to affect hemodynamics. Second, using large deformation diffeomorphic metric curve mapping (LDDMCM) to quantify pairwise shape similarity. We processed 96 images acquired with 3D rotational angiography. ICA identification had a cross-validation success rate of 99%. Automated landmarking was validated by computing limits of agreement with the reference taken to be the locations of the manually placed landmarks averaged across multiple observers. For all but one landmark, either the bias was not statistically significant or the variability was within 50% of the inter-observer one. The subsequently computed values of geometric features and LDDMCM were commensurate to the ones obtained with manual landmarking. The characterization based on pair-wise LDDMCM proved better in classifying the carotid siphon shape classes than the one based on geometric features. The proposed characterization provides a rich description of geometry and is ready to be applied in the search for geometric risk factors of the carotid siphon. Copyright © 2012 Elsevier B.V. All rights reserved.

MSAViewer: interactive JavaScript visualization of multiple sequence alignments.

PubMed

Yachdav, Guy; Wilzbach, Sebastian; Rauscher, Benedikt; Sheridan, Robert; Sillitoe, Ian; Procter, James; Lewis, Suzanna E; Rost, Burkhard; Goldberg, Tatyana

2016-11-15

The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is 'web ready': written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components. The MSAViewer is released as open source software under the Boost Software License 1.0. Documentation, source code and the viewer are available at http://msa.biojs.net/Supplementary information: Supplementary data are available at Bioinformatics online. msa@bio.sh. © The Author 2016. Published by Oxford University Press.

Investigation of Proposed Process Sequence for the Array Automated Assembly Task, Phase 2. [low cost silicon solar array fabrication

NASA Technical Reports Server (NTRS)

Mardesich, N.; Garcia, A.; Bunyan, S.; Pepe, A.

1979-01-01

The technological readiness of the proposed process sequence was reviewed. Process steps evaluated include: (1) plasma etching to establish a standard surface; (2) forming junctions by diffusion from an N-type polymeric spray-on source; (3) forming a p+ back contact by firing a screen printed aluminum paste; (4) forming screen printed front contacts after cleaning the back aluminum and removing the diffusion oxide; (5) cleaning the junction by a laser scribe operation; (6) forming an antireflection coating by baking a polymeric spray-on film; (7) ultrasonically tin padding the cells; and (8) assembling cell strings into solar circuits using ethylene vinyl acetate as an encapsulant and laminating medium.

AVTA federal fleet PEV readiness data logging and characterization study for the National Park Service: Grand Canyon National Park

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

Schey, Stephen; Francfort, Jim; Nienhueser, Ian

This report focuses on the Grand Canyon National Park (GCNP) fleet to identify daily operational characteristics of select vehicles and report findings on vehicle and mission characterizations to support the successful introduction of PEVs into the agencies’ fleets. Individual observations of these selected vehicles provide the basis for recommendations related to electric vehicle adoption and whether a battery electric vehicle or plug-in hybrid electric vehicle (collectively PEVs) can fulfill the mission requirements.

Ultrafast DNA sequencing on a microchip by a hybrid separation mechanism that gives 600 bases in 6.5 minutes.

PubMed

Fredlake, Christopher P; Hert, Daniel G; Kan, Cheuk-Wai; Chiesl, Thomas N; Root, Brian E; Forster, Ryan E; Barron, Annelise E

2008-01-15

To realize the immense potential of large-scale genomic sequencing after the completion of the second human genome (Venter's), the costs for the complete sequencing of additional genomes must be dramatically reduced. Among the technologies being developed to reduce sequencing costs, microchip electrophoresis is the only new technology ready to produce the long reads most suitable for the de novo sequencing and assembly of large and complex genomes. Compared with the current paradigm of capillary electrophoresis, microchip systems promise to reduce sequencing costs dramatically by increasing throughput, reducing reagent consumption, and integrating the many steps of the sequencing pipeline onto a single platform. Although capillary-based systems require approximately 70 min to deliver approximately 650 bases of contiguous sequence, we report sequencing up to 600 bases in just 6.5 min by microchip electrophoresis with a unique polymer matrix/adsorbed polymer wall coating combination. This represents a two-thirds reduction in sequencing time over any previously published chip sequencing result, with comparable read length and sequence quality. We hypothesize that these ultrafast long reads on chips can be achieved because the combined polymer system engenders a recently discovered "hybrid" mechanism of DNA electromigration, in which DNA molecules alternate rapidly between repeating through the intact polymer network and disrupting network entanglements to drag polymers through the solution, similar to dsDNA dynamics we observe in single-molecule DNA imaging studies. Most importantly, these results reveal the surprisingly powerful ability of microchip electrophoresis to provide ultrafast Sanger sequencing, which will translate to increased system throughput and reduced costs.

Ultrafast DNA sequencing on a microchip by a hybrid separation mechanism that gives 600 bases in 6.5 minutes

PubMed Central

Fredlake, Christopher P.; Hert, Daniel G.; Kan, Cheuk-Wai; Chiesl, Thomas N.; Root, Brian E.; Forster, Ryan E.; Barron, Annelise E.

2008-01-01

To realize the immense potential of large-scale genomic sequencing after the completion of the second human genome (Venter's), the costs for the complete sequencing of additional genomes must be dramatically reduced. Among the technologies being developed to reduce sequencing costs, microchip electrophoresis is the only new technology ready to produce the long reads most suitable for the de novo sequencing and assembly of large and complex genomes. Compared with the current paradigm of capillary electrophoresis, microchip systems promise to reduce sequencing costs dramatically by increasing throughput, reducing reagent consumption, and integrating the many steps of the sequencing pipeline onto a single platform. Although capillary-based systems require ≈70 min to deliver ≈650 bases of contiguous sequence, we report sequencing up to 600 bases in just 6.5 min by microchip electrophoresis with a unique polymer matrix/adsorbed polymer wall coating combination. This represents a two-thirds reduction in sequencing time over any previously published chip sequencing result, with comparable read length and sequence quality. We hypothesize that these ultrafast long reads on chips can be achieved because the combined polymer system engenders a recently discovered “hybrid” mechanism of DNA electromigration, in which DNA molecules alternate rapidly between reptating through the intact polymer network and disrupting network entanglements to drag polymers through the solution, similar to dsDNA dynamics we observe in single-molecule DNA imaging studies. Most importantly, these results reveal the surprisingly powerful ability of microchip electrophoresis to provide ultrafast Sanger sequencing, which will translate to increased system throughput and reduced costs. PMID:18184818

Microbiome and Bile Acid Profiles in Duodenal Aspirates from Cirrhotics: The Microbiome, Microbial Markers and Liver Disease Study.

PubMed

Jacobs, Jonathan P; Dong, Tien S; Agopian, Vatche; Lagishetty, Venu; Sundaram, Vinay; Noureddin, Mazen; Ayoub, Walid; Durazo, Francisco; Benhammou, Jihane; Enayati, Pedram; Elashoff, David; Goodman, Marc T; Pisegna, Joseph; Hussain, Shehnaz

2018-06-20

Cirrhosis is a leading cause of death in the world, yet there are no well-established risk stratifying tools for lethal complications including hepatocellular carcinoma (HCC). Patients with liver cirrhosis undergo routine endoscopic surveillance, providing ready access to duodenal aspirate samples which may be a source for identifying novel biomarkers. The aim of this study was to characterize the microbiome and bile acid profiles in duodenal aspirates from patients with liver cirrhosis to demonstrate feasibility of developing biomarkers for HCC risk stratification. Thirty patients with liver cirrhosis were enrolled in the Microbiome, Microbial Markers, and Liver Disease (M 3 LD) study between May 2015 and March 2017. Detailed clinical and epidemiological data were collected at baseline and at 6-monthly follow-up visits. Duodenal aspirate fluid was collected at baseline for microbial characterization using 16S ribosomal RNA sequencing and bile acid quantification using mass spectroscopy. Alcohol-related cirrhosis was associated with reductions in the Bacteroidetes phylum, particularly Prevotella (13-fold reduction), and expansion of Staphylococcus (13-fold increase), compared to HCV-related cirrhosis. Participants with hepatic encephalopathy (HE) had less microbial diversity compared to patients without HE (p<0.05), and were characterized by expansion of Mycobacterium (45-fold increase) and Gram positive cocci including Granulicatella (3.1-fold increase), unclassified Planococcaceae (3.3-fold increase), and unclassified Streptococcaceae (4.5-fold increase). Non-Hispanic Whites had reduced microbial richness (p<0.01) and diversity (p<0.05), and increased levels of conjugated ursodeoxycholic acid (glycoursodeoxycholic acid and tauroursodeoxycholic acid, p<0.05) compared to Hispanics. Microbial profiles of duodenal aspirates differed by cirrhosis etiology, HE, and Hispanic ethnicity. This article is protected by copyright. All rights reserved.

Assessing Organizational Readiness for a Participatory Occupational Health/Health Promotion Intervention in Skilled Nursing Facilities.

PubMed

Zhang, Yuan; Flum, Marian; West, Cheryl; Punnett, Laura

2015-09-01

The long-term care sector is characterized by high morbidity and employee turnover, along with associated costs. Effective health protection and health promotion are important to improve physical and psychosocial well-being of caregivers. Assessment of organizational readiness for change is an essential precursor to the successful implementation of workplace programs addressing work climate, structure of tasks and relationships, and other issues that may be perceived as challenging by some within the institution. This study qualitatively assessed readiness of five skilled nursing facilities for a participatory occupational health/health promotion intervention. Selection criteria were developed to screen for program feasibility and ability to conduct prospective evaluations, and information was collected from managers and employees (interviews and focus groups). Three centers were selected for the program, and the first year of formative evaluation and intervention experience was then reviewed to evaluate and modify our selection criteria after the fact. Lessons learned include adding assessment of communication and the structure of problem solving to our selection criteria, improving methods to assess management support in a concrete (potentially nonverbal) form, and obtaining a stated financial commitment and resources to enable the team to function. Assessment of organizational readiness for change is challenging, although necessary to implement effective and sustainable health promotion programs in specific organizations. © 2015 Society for Public Health Education.

Responding to Hostility: Evidence-Based Guidance for Communication during Planned Organizational Change

ERIC Educational Resources Information Center

Campbell, Kim Sydow; Carmichael, Pierson; Naidoo, Jefrey S.

2015-01-01

Hostile challenges to planned organization change are common and challenging to deal with effectively. Little research has explained successful responses to such stakeholder hostility. To address this gap, we use the concept of readiness to characterize the content of hostile challenges. We also use rhetorical strategies based on speech act theory…

Getting Ready to Read with Readers Theatre

ERIC Educational Resources Information Center

Barchers, Suzanne I; Pfeffinger, Charla R.

2007-01-01

Readers theatre is a presentation by two or more participants who read from scripts and interpret a literary work in such a way that the audience imaginatively senses characterization, setting, and action. This book offers 50, two-page reproducible scripts to entice the preschool and kindergarten group into beginning to read. These patterned…

Effective Teaching: Preparation and Implementation. Fourth Edition

ERIC Educational Resources Information Center

Hunt, Gilbert H.; Wiseman, Dennis G.; Touzel, Timothy J.

2009-01-01

Schools today have transcended from the chalkboard to the whiteboard and are populated by students who are not frightened to use the technology of this new age of learning. During this period of dynamic change, teachers must be ready to meet the challenges of preparing students for a global society characterized by diversity and ever-increasing…

Streamlining the Design-to-Build Transition with Build-Optimization Software Tools.

PubMed

Oberortner, Ernst; Cheng, Jan-Fang; Hillson, Nathan J; Deutsch, Samuel

2017-03-17

Scaling-up capabilities for the design, build, and test of synthetic biology constructs holds great promise for the development of new applications in fuels, chemical production, or cellular-behavior engineering. Construct design is an essential component in this process; however, not every designed DNA sequence can be readily manufactured, even using state-of-the-art DNA synthesis methods. Current biological computer-aided design and manufacture tools (bioCAD/CAM) do not adequately consider the limitations of DNA synthesis technologies when generating their outputs. Designed sequences that violate DNA synthesis constraints may require substantial sequence redesign or lead to price-premiums and temporal delays, which adversely impact the efficiency of the DNA manufacturing process. We have developed a suite of build-optimization software tools (BOOST) to streamline the design-build transition in synthetic biology engineering workflows. BOOST incorporates knowledge of DNA synthesis success determinants into the design process to output ready-to-build sequences, preempting the need for sequence redesign. The BOOST web application is available at https://boost.jgi.doe.gov and its Application Program Interfaces (API) enable integration into automated, customized DNA design processes. The herein presented results highlight the effectiveness of BOOST in reducing DNA synthesis costs and timelines.

Molecular Characterization of Transgenic Events Using Next Generation Sequencing Approach.

PubMed

Guttikonda, Satish K; Marri, Pradeep; Mammadov, Jafar; Ye, Liang; Soe, Khaing; Richey, Kimberly; Cruse, James; Zhuang, Meibao; Gao, Zhifang; Evans, Clive; Rounsley, Steve; Kumpatla, Siva P

2016-01-01

Demand for the commercial use of genetically modified (GM) crops has been increasing in light of the projected growth of world population to nine billion by 2050. A prerequisite of paramount importance for regulatory submissions is the rigorous safety assessment of GM crops. One of the components of safety assessment is molecular characterization at DNA level which helps to determine the copy number, integrity and stability of a transgene; characterize the integration site within a host genome; and confirm the absence of vector DNA. Historically, molecular characterization has been carried out using Southern blot analysis coupled with Sanger sequencing. While this is a robust approach to characterize the transgenic crops, it is both time- and resource-consuming. The emergence of next-generation sequencing (NGS) technologies has provided highly sensitive and cost- and labor-effective alternative for molecular characterization compared to traditional Southern blot analysis. Herein, we have demonstrated the successful application of both whole genome sequencing and target capture sequencing approaches for the characterization of single and stacked transgenic events and compared the results and inferences with traditional method with respect to key criteria required for regulatory submissions.

Sequence Variations in the Flagellar Antigen Genes fliCH25 and fliCH28 of Escherichia coli and Their Use in Identification and Characterization of Enterohemorrhagic E. coli (EHEC) O145:H25 and O145:H28.

PubMed

Beutin, Lothar; Delannoy, Sabine; Fach, Patrick

2015-01-01

Enterohemorrhagic E. coli (EHEC) serogroup O145 is regarded as one of the major EHEC serogroups involved in severe infections in humans. EHEC O145 encompasses motile and non-motile strains of serotypes O145:H25 and O145:H28. Sequencing the fliC-genes associated with the flagellar antigens H25 and H28 revealed the genetic diversity of the fliCH25 and fliCH28 gene sequences in E. coli. Based on allele discrimination of these fliC-genes real-time PCR tests were designed for identification of EHEC O145:H25 and O145:H28. The fliCH25 genes present in O145:H25 were found to be very similar to those present in E. coli serogroups O2, O100, O165, O172 and O177 pointing to their common evolution but were different from fliCH25 genes of a multiple number of other E. coli serotypes. In a similar way, EHEC O145:H28 harbor a characteristic fliCH28 allele which, apart from EHEC O145:H28, was only found in enteropathogenic (EPEC) O28:H28 strains that shared some common traits with EHEC O145:H28. The real time PCR-assays targeting these fliCH25[O145] and fliCH28[O145] alleles allow better characterization of EHEC O145:H25 and EHEC O145:H28. Evaluation of these PCR assays in spiked ready-to eat salad samples resulted in specific detection of both types of EHEC O145 strains even when low spiking levels of 1-10 cfu/g were used. Furthermore these PCR assays allowed identification of non-motile E. coli strains which are serologically not typable for their H-antigens. The combined use of O-antigen genotyping (O145wzy) and detection of the respective fliCH25[O145] and fliCH28[O145] allele types contributes to improve identification and molecular serotyping of E. coli O145 isolates.

Sequence Variations in the Flagellar Antigen Genes fliC H25 and fliC H28 of Escherichia coli and Their Use in Identification and Characterization of Enterohemorrhagic E. coli (EHEC) O145:H25 and O145:H28

PubMed Central

Beutin, Lothar; Delannoy, Sabine; Fach, Patrick

2015-01-01

Enterohemorrhagic E. coli (EHEC) serogroup O145 is regarded as one of the major EHEC serogroups involved in severe infections in humans. EHEC O145 encompasses motile and non-motile strains of serotypes O145:H25 and O145:H28. Sequencing the fliC-genes associated with the flagellar antigens H25 and H28 revealed the genetic diversity of the fliC H25 and fliC H28 gene sequences in E. coli. Based on allele discrimination of these fliC-genes real-time PCR tests were designed for identification of EHEC O145:H25 and O145:H28. The fliC H25 genes present in O145:H25 were found to be very similar to those present in E. coli serogroups O2, O100, O165, O172 and O177 pointing to their common evolution but were different from fliC H25 genes of a multiple number of other E. coli serotypes. In a similar way, EHEC O145:H28 harbor a characteristic fliC H28 allele which, apart from EHEC O145:H28, was only found in enteropathogenic (EPEC) O28:H28 strains that shared some common traits with EHEC O145:H28. The real time PCR-assays targeting these fliC H25[O145] and fliC H28[O145] alleles allow better characterization of EHEC O145:H25 and EHEC O145:H28. Evaluation of these PCR assays in spiked ready-to eat salad samples resulted in specific detection of both types of EHEC O145 strains even when low spiking levels of 1–10 cfu/g were used. Furthermore these PCR assays allowed identification of non-motile E. coli strains which are serologically not typable for their H-antigens. The combined use of O-antigen genotyping (O145wzy) and detection of the respective fliC H25[O145] and fliC H28[O145] allele types contributes to improve identification and molecular serotyping of E. coli O145 isolates. PMID:26000885

Characterization of a broad host-spectrum virulent Salmonella bacteriophage fmb-p1 and its application on duck meat.

PubMed

Wang, Changbao; Chen, Qiming; Zhang, Chong; Yang, Jie; Lu, Zhaoxin; Lu, Fengxia; Bie, Xiaomei

2017-05-15

The aim of this study was to find a virulent bacteriophage for the biocontrol of Salmonella in duck meat. A broad host-spectrum virulent phage, fmb-p1, was isolated and purified from an duck farm, and its host range was determined to include S. Typhimurium, S. Enteritidis, S. Saintpaul, S. Agona, S. Miami, S. Anatum, S. Heidelberg and S. Paratyphi-C. Electron microscopy and genome sequencing showed that fmb-p1 belongs to the family Siphoviridae. The genome of fmb-p1 is composed of a 43,327-bp double-stranded DNA molecule with 60 open reading frames and a total G+C content of 46.09%. There are no deleterious sequences or genes encoding known harmful products in the phage fmb-p1 genome. Phage fmb-p1 was stable under different temperature (40-75°C), pH (4-10) and NaCl solutions (1-11%). The phage treatment (9.9×10 9 PFU/cm 2 ) caused a peak reduction in S. Typhimurium of 4.52 log CFU/cm 2 in ready-to-eat (RTE) duck meat, whereas potassium sorbate treatment (PS, 2mg/cm 2 ) resulted in a 0.05-0.12 log reduction. Compared to PS treatment, there was significant difference in the S. Typhimurium reduction (P˂0.05) by phage treatment at both 4°C and 25°C. The results suggested that phage could be applied to reduce Salmonella, on commercial poultry products. Copyright © 2017 Elsevier B.V. All rights reserved.

From carbon to actinides: A new universal 1MV accelerator mass spectrometer at ANSTO

NASA Astrophysics Data System (ADS)

Wilcken, K. M.; Hotchkis, M.; Levchenko, V.; Fink, D.; Hauser, T.; Kitchen, R.

2015-10-01

A new 1 MV NEC pelletron AMS system at ANSTO is presented. The spectrometer comprises large radius magnets for actinide measurements. A novel feature of the system is fast switching between isotopes both at low and high energy sections allowing measurements of up to 8 isotopes within a single sequence. Technical details and layout of the spectrometer is presented. Performance data for 14C, 10Be, 26Al and actinides demonstrate the system is ready for routine AMS measurements.

Synthesis of mucin-type O-glycan probes as aminopropyl glycosides.

PubMed

Benito-Alifonso, David; Jones, Rachel A; Tran, Anh-Tuan; Woodward, Hannah; Smith, Nichola; Galan, M Carmen

2013-01-01

The chemical synthesis of a series of mucin-type oligosaccharide fragments 1-7 containing an α-linked aminopropyl spacer ready for glycoarray attachment is reported. A highly convergent and stereoselective strategy that employs two different orthogonal protected galactosamine building blocks was used to access all of the targets. A tandem deprotection sequence, that did not require chromatography-based purification between steps, was employed to globally unmask all protecting groups and all final targets were isolated in good to excellent yields.

The establishment of a production-ready manufacturing process utilizing thin silicon substrates for solar cells

NASA Technical Reports Server (NTRS)

Pryor, R. A.

1980-01-01

Three inch diameter Czochralski silicon substrates sliced directly to 5 mil, 8 mil, and 27 mil thicknesses with wire saw techniques were procured. Processing sequences incorporating either diffusion or ion implantation technologies were employed to produce n+p or n+pp+ solar cell structures. These cells were evaluated for performance, ease of fabrication, and cost effectiveness. It was determined that the use of 7 mil or even 4 mil wafers would provide near term cost reductions for solar cell manufacturers.

Approximating the Basset force by optimizing the method of van Hinsberg et al.

NASA Astrophysics Data System (ADS)

Casas, G.; Ferrer, A.; Oñate, E.

2018-01-01

In this work we put the method proposed by van Hinsberg et al. [29] to the test, highlighting its accuracy and efficiency in a sequence of benchmarks of increasing complexity. Furthermore, we explore the possibility of systematizing the way in which the method's free parameters are determined by generalizing the optimization problem that was considered originally. Finally, we provide a list of worked-out values, ready for implementation in large-scale particle-laden flow simulations.

Prescreening of microbial populations for the assessment of sequencing potential.

PubMed

Hanning, Irene B; Ricke, Steven C

2011-01-01

Next-generation sequencing (NGS) is a powerful tool that can be utilized to profile and compare microbial populations. By amplifying a target gene present in all bacteria and subsequently sequencing amplicons, the bacteria genera present in the populations can be identified and compared. In some scenarios, little to no difference may exist among microbial populations being compared in which case a prescreening method would be practical to determine which microbial populations would be suitable for further analysis by NGS. Denaturing density-gradient electrophoresis (DGGE) is relatively cheaper than NGS and the data comparing microbial populations are ready to be viewed immediately after electrophoresis. DGGE follows essentially the same initial methodology as NGS by targeting and amplifying the 16S rRNA gene. However, as opposed to sequencing amplicons, DGGE amplicons are analyzed by electrophoresis. By prescreening microbial populations with DGGE, more efficient use of NGS methods can be accomplished. In this chapter, we outline the protocol for DGGE targeting the same gene (16S rRNA) that would be targeted for NGS to compare and determine differences in microbial populations from a wide range of ecosystems.

The draft genome sequence of cork oak

PubMed Central

Ramos, António Marcos; Usié, Ana; Barbosa, Pedro; Barros, Pedro M.; Capote, Tiago; Chaves, Inês; Simões, Fernanda; Abreu, Isabl; Carrasquinho, Isabel; Faro, Carlos; Guimarães, Joana B.; Mendonça, Diogo; Nóbrega, Filomena; Rodrigues, Leandra; Saibo, Nelson J. M.; Varela, Maria Carolina; Egas, Conceição; Matos, José; Miguel, Célia M.; Oliveira, M. Margarida; Ricardo, Cândido P.; Gonçalves, Sónia

2018-01-01

Cork oak (Quercus suber) is native to southwest Europe and northwest Africa where it plays a crucial environmental and economical role. To tackle the cork oak production and industrial challenges, advanced research is imperative but dependent on the availability of a sequenced genome. To address this, we produced the first draft version of the cork oak genome. We followed a de novo assembly strategy based on high-throughput sequence data, which generated a draft genome comprising 23,347 scaffolds and 953.3 Mb in size. A total of 79,752 genes and 83,814 transcripts were predicted, including 33,658 high-confidence genes. An InterPro signature assignment was detected for 69,218 transcripts, which represented 82.6% of the total. Validation studies demonstrated the genome assembly and annotation completeness and highlighted the usefulness of the draft genome for read mapping of high-throughput sequence data generated using different protocols. All data generated is available through the public databases where it was deposited, being therefore ready to use by the academic and industry communities working on cork oak and/or related species. PMID:29786699

The draft genome sequence of cork oak.

PubMed

Ramos, António Marcos; Usié, Ana; Barbosa, Pedro; Barros, Pedro M; Capote, Tiago; Chaves, Inês; Simões, Fernanda; Abreu, Isabl; Carrasquinho, Isabel; Faro, Carlos; Guimarães, Joana B; Mendonça, Diogo; Nóbrega, Filomena; Rodrigues, Leandra; Saibo, Nelson J M; Varela, Maria Carolina; Egas, Conceição; Matos, José; Miguel, Célia M; Oliveira, M Margarida; Ricardo, Cândido P; Gonçalves, Sónia

2018-05-22

Cork oak (Quercus suber) is native to southwest Europe and northwest Africa where it plays a crucial environmental and economical role. To tackle the cork oak production and industrial challenges, advanced research is imperative but dependent on the availability of a sequenced genome. To address this, we produced the first draft version of the cork oak genome. We followed a de novo assembly strategy based on high-throughput sequence data, which generated a draft genome comprising 23,347 scaffolds and 953.3 Mb in size. A total of 79,752 genes and 83,814 transcripts were predicted, including 33,658 high-confidence genes. An InterPro signature assignment was detected for 69,218 transcripts, which represented 82.6% of the total. Validation studies demonstrated the genome assembly and annotation completeness and highlighted the usefulness of the draft genome for read mapping of high-throughput sequence data generated using different protocols. All data generated is available through the public databases where it was deposited, being therefore ready to use by the academic and industry communities working on cork oak and/or related species.

A sequence-based survey of the complex structural organization of tumor genomes

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

Collins, Colin; Raphael, Benjamin J.; Volik, Stanislav

2008-04-03

The genomes of many epithelial tumors exhibit extensive chromosomal rearrangements. All classes of genome rearrangements can be identified using End Sequencing Profiling (ESP), which relies on paired-end sequencing of cloned tumor genomes. In this study, brain, breast, ovary and prostate tumors along with three breast cancer cell lines were surveyed with ESP yielding the largest available collection of sequence-ready tumor genome breakpoints and providing evidence that some rearrangements may be recurrent. Sequencing and fluorescence in situ hybridization (FISH) confirmed translocations and complex tumor genome structures that include coamplification and packaging of disparate genomic loci with associated molecular heterogeneity. Comparison ofmore » the tumor genomes suggests recurrent rearrangements. Some are likely to be novel structural polymorphisms, whereas others may be bona fide somatic rearrangements. A recurrent fusion transcript in breast tumors and a constitutional fusion transcript resulting from a segmental duplication were identified. Analysis of end sequences for single nucleotide polymorphisms (SNPs) revealed candidate somatic mutations and an elevated rate of novel SNPs in an ovarian tumor. These results suggest that the genomes of many epithelial tumors may be far more dynamic and complex than previously appreciated and that genomic fusions including fusion transcripts and proteins may be common, possibly yielding tumor-specific biomarkers and therapeutic targets.« less

Study of the Technical Feasibility of Increasing the Amount of Recycled Concrete Waste Used in Ready-Mix Concrete Production

PubMed Central

Ferreiro-Cabello, Javier; López-González, Luis M.

2017-01-01

The construction industry generates a considerable amount of waste. Faced with this undesirable situation, the ready-mix concrete sector, in particular, has invested energy and resources into reusing its own waste in its production process as it works towards the goal of more sustainable construction. This study examines the feasibility of incorporating two types of concrete waste, which currently end up in landfill, into the production process of ready-mix concrete: the waste generated during the initial production stage (ready-mix concrete waste), and waste created when demolition waste is treated to obtain artificial aggregate. The first phase of the study’s methodology corroborates the suitability of the recycled aggregate through characterization tests. After this phase, the impact of incorporating different percentages of recycled coarse aggregate is evaluated by examining the performance of the produced concrete. The replacement rate varied between 15% and 50%. The results indicate that recycled aggregates are, indeed, suitable to be incorporated into ready-mix concrete production. The impact on the final product’s performance is different for the two cases examined herein. Incorporating aggregates from generic concrete blocks led to a 20% decrease in the produced concrete’s strength performance. On the other hand, using recycled aggregates made from the demolition waste led to a smaller decrease in the concrete’s performance: about 8%. The results indicate that with adequate management and prior treatment, the waste from these plants can be re-incorporated into their production processes. If concrete waste is re-used, concrete production, in general, becomes more sustainable for two reasons: less waste ends up as landfill and the consumption of natural aggregates is also reduced. PMID:28773183

Study of the Technical Feasibility of Increasing the Amount of Recycled Concrete Waste Used in Ready-Mix Concrete Production.

PubMed

Fraile-Garcia, Esteban; Ferreiro-Cabello, Javier; López-Ochoa, Luis M; López-González, Luis M

2017-07-18

The construction industry generates a considerable amount of waste. Faced with this undesirable situation, the ready-mix concrete sector, in particular, has invested energy and resources into reusing its own waste in its production process as it works towards the goal of more sustainable construction. This study examines the feasibility of incorporating two types of concrete waste, which currently end up in landfill, into the production process of ready-mix concrete: the waste generated during the initial production stage (ready-mix concrete waste), and waste created when demolition waste is treated to obtain artificial aggregate. The first phase of the study's methodology corroborates the suitability of the recycled aggregate through characterization tests. After this phase, the impact of incorporating different percentages of recycled coarse aggregate is evaluated by examining the performance of the produced concrete. The replacement rate varied between 15% and 50%. The results indicate that recycled aggregates are, indeed, suitable to be incorporated into ready-mix concrete production. The impact on the final product's performance is different for the two cases examined herein. Incorporating aggregates from generic concrete blocks led to a 20% decrease in the produced concrete's strength performance. On the other hand, using recycled aggregates made from the demolition waste led to a smaller decrease in the concrete's performance: about 8%. The results indicate that with adequate management and prior treatment, the waste from these plants can be re-incorporated into their production processes. If concrete waste is re-used, concrete production, in general, becomes more sustainable for two reasons: less waste ends up as landfill and the consumption of natural aggregates is also reduced.

76 FR 38618 - Proposed Information Collection; Comment Request; StormReadyTM

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-01

... Collection; Comment Request; StormReady\\TM\\, TsunamiReady\\TM\\ and StormReady/TsunamiReady\\TM\\ Application... information collection. The StormReady Program, like the TsunamiReady and StormReady/TsunamiReady programs... certain guidelines that qualify them for StormReady recognition. The full StormReady recognition is not...

An investigation of articulatory setting using real-time magnetic resonance imaging

PubMed Central

Ramanarayanan, Vikram; Goldstein, Louis; Byrd, Dani; Narayanan, Shrikanth S.

2013-01-01

This paper presents an automatic procedure to analyze articulatory setting in speech production using real-time magnetic resonance imaging of the moving human vocal tract. The procedure extracts frames corresponding to inter-speech pauses, speech-ready intervals and absolute rest intervals from magnetic resonance imaging sequences of read and spontaneous speech elicited from five healthy speakers of American English and uses automatically extracted image features to quantify vocal tract posture during these intervals. Statistical analyses show significant differences between vocal tract postures adopted during inter-speech pauses and those at absolute rest before speech; the latter also exhibits a greater variability in the adopted postures. In addition, the articulatory settings adopted during inter-speech pauses in read and spontaneous speech are distinct. The results suggest that adopted vocal tract postures differ on average during rest positions, ready positions and inter-speech pauses, and might, in that order, involve an increasing degree of active control by the cognitive speech planning mechanism. PMID:23862826

Microbes, metagenomes and marine mammals: enabling the next generation of scientist to enter the genomic era

PubMed Central

2013-01-01

Background The revolution in DNA sequencing technology continues unabated, and is affecting all aspects of the biological and medical sciences. The training and recruitment of the next generation of researchers who are able to use and exploit the new technology is severely lacking and potentially negatively influencing research and development efforts to advance genome biology. Here we present a cross-disciplinary course that provides undergraduate students with practical experience in running a next generation sequencing instrument through to the analysis and annotation of the generated DNA sequences. Results Many labs across world are installing next generation sequencing technology and we show that the undergraduate students produce quality sequence data and were excited to participate in cutting edge research. The students conducted the work flow from DNA extraction, library preparation, running the sequencing instrument, to the extraction and analysis of the data. They sequenced microbes, metagenomes, and a marine mammal, the Californian sea lion, Zalophus californianus. The students met sequencing quality controls, had no detectable contamination in the targeted DNA sequences, provided publication quality data, and became part of an international collaboration to investigate carcinomas in carnivores. Conclusions Students learned important skills for their future education and career opportunities, and a perceived increase in students’ ability to conduct independent scientific research was measured. DNA sequencing is rapidly expanding in the life sciences. Teaching undergraduates to use the latest technology to sequence genomic DNA ensures they are ready to meet the challenges of the genomic era and allows them to participate in annotating the tree of life. PMID:24007365

Variable sequences outside the SAM-binding core critically influence the conformational dynamics of the SAM-III/SMK box riboswitch

PubMed Central

Lu, Changrui; Smith, Angela M; Ding, Fang; Chowdhury, Anirban; Henkin, Tina M; Ke, Ailong

2012-01-01

The SMK box (SAM-III) translational riboswitches were identified in S-adenosyl-L-methionine (SAM) synthetase metK genes in members of the Lactobacillales. This riboswitch switches between two alternative conformations in response to the intracellular SAM concentration and controls metK expression at the level of translation initiation. We previously reported the crystal structure of the SAM-bound SMK box riboswitch. In this study we combined SHAPE chemical probing with mutagenesis to probe the ligand-induced conformational switching mechanism. We revealed that while the majority of the apo SMK box RNA molecules exist in an alternatively base paired (ON) conformation, a subset of them pre-organize into a SAM-bound-like (READY) conformation, which upon SAM exposure is selectively stabilized into the SAM-bound (OFF) conformation through an induced-fit mechanism. Mutagenesis showed that the ON state is only slightly more stable than the READY state, as several single-nucleotide substitutions in a hypervariable region outside the SAM-binding core can alter the folding landscape to favor the READY state. Such SMK variants display a “constitutively-OFF” behavior both in vitro and in vivo. Time-resolved and temperature-dependent SHAPE analyses revealed adaptation of the SMK box RNA to its mesothermal working environment. The latter analysis revealed that the SAM-bound SMK box RNA follows a two-step folding/unfolding process. PMID:21549712

Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community.

PubMed

Ciric, Milica; Moon, Christina D; Leahy, Sinead C; Creevey, Christopher J; Altermann, Eric; Attwood, Graeme T; Rakonjac, Jasna; Gagic, Dragana

2014-05-12

In silico, secretome proteins can be predicted from completely sequenced genomes using various available algorithms that identify membrane-targeting sequences. For metasecretome (collection of surface, secreted and transmembrane proteins from environmental microbial communities) this approach is impractical, considering that the metasecretome open reading frames (ORFs) comprise only 10% to 30% of total metagenome, and are poorly represented in the dataset due to overall low coverage of metagenomic gene pool, even in large-scale projects. By combining secretome-selective phage display and next-generation sequencing, we focused the sequence analysis of complex rumen microbial community on the metasecretome component of the metagenome. This approach achieved high enrichment (29 fold) of secreted fibrolytic enzymes from the plant-adherent microbial community of the bovine rumen. In particular, we identified hundreds of heretofore rare modules belonging to cellulosomes, cell-surface complexes specialised for recognition and degradation of the plant fibre. As a method, metasecretome phage display combined with next-generation sequencing has a power to sample the diversity of low-abundance surface and secreted proteins that would otherwise require exceptionally large metagenomic sequencing projects. As a resource, metasecretome display library backed by the dataset obtained by next-generation sequencing is ready for i) affinity selection by standard phage display methodology and ii) easy purification of displayed proteins as part of the virion for individual functional analysis.

Analysis of genetically modified organisms by pyrosequencing on a portable photodiode-based bioluminescence sequencer.

PubMed

Song, Qinxin; Wei, Guijiang; Zhou, Guohua

2014-07-01

A portable bioluminescence analyser for detecting the DNA sequence of genetically modified organisms (GMOs) was developed by using a photodiode (PD) array. Pyrosequencing on eight genes (zSSIIb, Bt11 and Bt176 gene of genetically modified maize; Lectin, 35S-CTP4, CP4EPSPS, CaMV35S promoter and NOS terminator of the genetically modified Roundup ready soya) was successfully detected with this instrument. The corresponding limit of detection (LOD) was 0.01% with 35 PCR cycles. The maize and soya available from three different provenances in China were detected. The results indicate that pyrosequencing using the small size of the detector is a simple, inexpensive, and reliable way in a farm/field test of GMO analysis. Copyright © 2014 Elsevier Ltd. All rights reserved.

Skin Microbiome Surveys Are Strongly Influenced by Experimental Design.

PubMed

Meisel, Jacquelyn S; Hannigan, Geoffrey D; Tyldsley, Amanda S; SanMiguel, Adam J; Hodkinson, Brendan P; Zheng, Qi; Grice, Elizabeth A

2016-05-01

Culture-independent studies to characterize skin microbiota are increasingly common, due in part to affordable and accessible sequencing and analysis platforms. Compared to culture-based techniques, DNA sequencing of the bacterial 16S ribosomal RNA (rRNA) gene or whole metagenome shotgun (WMS) sequencing provides more precise microbial community characterizations. Most widely used protocols were developed to characterize microbiota of other habitats (i.e., gastrointestinal) and have not been systematically compared for their utility in skin microbiome surveys. Here we establish a resource for the cutaneous research community to guide experimental design in characterizing skin microbiota. We compare two widely sequenced regions of the 16S rRNA gene to WMS sequencing for recapitulating skin microbiome community composition, diversity, and genetic functional enrichment. We show that WMS sequencing most accurately recapitulates microbial communities, but sequencing of hypervariable regions 1-3 of the 16S rRNA gene provides highly similar results. Sequencing of hypervariable region 4 poorly captures skin commensal microbiota, especially Propionibacterium. WMS sequencing, which is resource and cost intensive, provides evidence of a community's functional potential; however, metagenome predictions based on 16S rRNA sequence tags closely approximate WMS genetic functional profiles. This study highlights the importance of experimental design for downstream results in skin microbiome surveys. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Skin microbiome surveys are strongly influenced by experimental design

PubMed Central

Meisel, Jacquelyn S.; Hannigan, Geoffrey D.; Tyldsley, Amanda S.; SanMiguel, Adam J.; Hodkinson, Brendan P.; Zheng, Qi; Grice, Elizabeth A.

2016-01-01

Culture-independent studies to characterize skin microbiota are increasingly common, due in part to affordable and accessible sequencing and analysis platforms. Compared to culture-based techniques, DNA sequencing of the bacterial 16S ribosomal RNA (rRNA) gene or whole metagenome shotgun (WMS) sequencing provide more precise microbial community characterizations. Most widely used protocols were developed to characterize microbiota of other habitats (i.e. gastrointestinal), and have not been systematically compared for their utility in skin microbiome surveys. Here we establish a resource for the cutaneous research community to guide experimental design in characterizing skin microbiota. We compare two widely sequenced regions of the 16S rRNA gene to WMS sequencing for recapitulating skin microbiome community composition, diversity, and genetic functional enrichment. We show that WMS sequencing most accurately recapitulates microbial communities, but sequencing of hypervariable regions 1-3 of the 16S rRNA gene provides highly similar results. Sequencing of hypervariable region 4 poorly captures skin commensal microbiota, especially Propionibacterium. WMS sequencing, which is resource- and cost-intensive, provides evidence of a community’s functional potential; however, metagenome predictions based on 16S rRNA sequence tags closely approximate WMS genetic functional profiles. This work highlights the importance of experimental design for downstream results in skin microbiome surveys. PMID:26829039

Evolving discriminators for querying video sequences

NASA Astrophysics Data System (ADS)

Iyengar, Giridharan; Lippman, Andrew B.

1997-01-01

In this paper we present a framework for content based query and retrieval of information from large video databases. This framework enables content based retrieval of video sequences by characterizing the sequences using motion, texture and colorimetry cues. This characterization is biologically inspired and results in a compact parameter space where every segment of video is represented by an 8 dimensional vector. Searching and retrieval is done in real- time with accuracy in this parameter space. Using this characterization, we then evolve a set of discriminators using Genetic Programming Experiments indicate that these discriminators are capable of analyzing and characterizing video. The VideoBook is able to search and retrieve video sequences with 92% accuracy in real-time. Experiments thus demonstrate that the characterization is capable of extracting higher level structure from raw pixel values.

Getting Ready for School: Palm Beach County's Early Childhood Cluster Initiative

ERIC Educational Resources Information Center

Spielberger, Julie; Baker, Stephen; Winje, Carolyn

2008-01-01

This publication reports findings from the second year of an implementation study of the Early Childhood Cluster Initiative (ECCI). ECCI is a prekindergarten program in ten elementary schools and a community child care center in Palm Beach County, based on the design of the High/Scope Perry Preschool model. The initiative is characterized by low…

Illinois STEM College and Career Readiness: Forging a Pathway to Postsecondary Education by Curbing Math Remediation. In Brief

ERIC Educational Resources Information Center

Baber, Lorenzo; Graham, Edmund; Taylor, Jason L.; Reese, George; Bragg, Debra D.; Lang, John; Zamani-Gallaher, Eboni M.

2015-01-01

In a knowledge-based economy, a postsecondary credential is vital for gainful employment and upward socioeconomic mobility. Unfortunately, the path a student takes from high school graduation to college course work is too often characterized by a troubling detour, namely, "remediation." According to Complete College America (2012), over…

AVTA Federal Fleet PEV Readiness Data Logging and Characterization Study for Department of Veterans Affairs – VA Manhattan Campus

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

Stephen Schey; Jim Francfort

2014-10-01

This report focuses on the Department of Veterans Affairs, VA Manhattan Campus (VA- Manhattan) fleet to identify the daily operational characteristics of select vehicles and report findings on vehicle and mission characterizations to support successful introduction of plug-in electric vehicles (PEVs) into the agency’s fleet. Individual observations of these selected vehicles provide the basis for recommendations related to electric vehicle adoption and whether a battery electric vehicle or plug-in hybrid electric vehicle (collectively called PEVs) can fulfill the mission requirements.

AVTA Federal Fleet PEV Readiness Data Logging and Characterization Study for NASA White Sands Test Facility

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

Schey, Stephen; Francfort, Jim

This report focuses on the NASA White Sands Test Facility (WSTF) fleet to identify daily operational characteristics of select vehicles and report findings on vehicle and mission characterizations to support the successful introduction of plug-in electric vehicles (PEVs) into the agencies’ fleets. Individual observations of these selected vehicles provide the basis for recommendations related to electric vehicle adoption and whether a battery electric vehicle (BEV) or plug-in hybrid electric vehicle (PHEV) (collectively plug-in electric vehicles, or PEVs) can fulfill the mission requirements.

AVTA Federal Fleet PEV Readiness Data Logging and Characterization Study for National Institute of Health

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

Schey, Stephen; Francfort, Jim

2014-11-01

This report focuses on the National Institute of Health (NIH) fleet to identify daily operational characteristics of select vehicles and report findings on vehicle and mission characterizations to support the successful introduction of plug-in electric vehicles (PEVs) into the agencies’ fleets. Individual observations of these selected vehicles provide the basis for recommendations related to electric vehicle adoption and whether a battery electric vehicle (BEV) or plug-in hybrid electric vehicle (PHEV) (collectively plug-in electric vehicles, or PEVs) can fulfill the mission requirements.

AVTA Federal Fleet PEV Readiness Data Logging and Characterization Study for Department of Health and Human Services – ASPR

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

Schey, Steve; Francfort, Jim

2015-06-01

This report focuses on the Department of Health and Human Services, Assistant Secretary for Preparedness and Response fleet to identify daily operational characteristics of select vehicles and report findings on vehicle and mission characterizations to support the successful introduction of PEVs into the agency’s fleet. Individual observations of these selected vehicles provide the basis for recommendations related to electric vehicle adoption and whether a battery electric vehicle or plug-in hybrid electric vehicle (collectively referred to as PEVs) can fulfill the mission requirements.

Development of a screening method for genetically modified soybean by plasmid-based quantitative competitive polymerase chain reaction.

PubMed

Shimizu, Eri; Kato, Hisashi; Nakagawa, Yuki; Kodama, Takashi; Futo, Satoshi; Minegishi, Yasutaka; Watanabe, Takahiro; Akiyama, Hiroshi; Teshima, Reiko; Furui, Satoshi; Hino, Akihiro; Kitta, Kazumi

2008-07-23

A novel type of quantitative competitive polymerase chain reaction (QC-PCR) system for the detection and quantification of the Roundup Ready soybean (RRS) was developed. This system was designed based on the advantage of a fully validated real-time PCR method used for the quantification of RRS in Japan. A plasmid was constructed as a competitor plasmid for the detection and quantification of genetically modified soy, RRS. The plasmid contained the construct-specific sequence of RRS and the taxon-specific sequence of lectin1 (Le1), and both had 21 bp oligonucleotide insertion in the sequences. The plasmid DNA was used as a reference molecule instead of ground seeds, which enabled us to precisely and stably adjust the copy number of targets. The present study demonstrated that the novel plasmid-based QC-PCR method could be a simple and feasible alternative to the real-time PCR method used for the quantification of genetically modified organism contents.

Multiplex nucleic acid sequence-based amplification for simultaneous detection of several enteric viruses in model ready-to-eat foods.

PubMed

Jean, Julie; D'Souza, Doris H; Jaykus, Lee-Ann

2004-11-01

Human enteric viruses are currently recognized as one of the most important causes of food-borne disease. Implication of enteric viruses in food-borne outbreaks can be difficult to confirm due to the inadequacy of the detection methods available. In this study, a nucleic acid sequence-based amplification (NASBA) method was developed in a multiplex format for the specific, simultaneous, and rapid detection of epidemiologically relevant human enteric viruses. Three previously reported primer sets were used in a single reaction for the amplification of RNA target fragments of 474, 371, and 165 nucleotides for the detection of hepatitis A virus and genogroup I and genogroup II noroviruses, respectively. Amplicons were detected by agarose gel electrophoresis and confirmed by electrochemiluminescence and Northern hybridization. Endpoint detection sensitivity for the multiplex NASBA assay was approximately 10(-1) reverse transcription-PCR-detectable units (or PFU, as appropriate) per reaction. When representative ready-to-eat foods (deli sliced turkey and lettuce) were inoculated with various concentrations of each virus and processed for virus detection with the multiplex NASBA method, all three human enteric viruses were simultaneously detected at initial inoculum levels of 10(0) to 10(2) reverse transcription-PCR-detectable units (or PFU)/9 cm2 in both food commodities. The multiplex NASBA system provides rapid and simultaneous detection of clinically relevant food-borne viruses in a single reaction tube and may be a promising alternative to reverse transcription-PCR for the detection of viral contamination of foods.

CDinFusion – Submission-Ready, On-Line Integration of Sequence and Contextual Data

PubMed Central

Hankeln, Wolfgang; Wendel, Norma Johanna; Gerken, Jan; Waldmann, Jost; Buttigieg, Pier Luigi; Kostadinov, Ivaylo; Kottmann, Renzo; Yilmaz, Pelin; Glöckner, Frank Oliver

2011-01-01

State of the art (DNA) sequencing methods applied in “Omics” studies grant insight into the ‘blueprints’ of organisms from all domains of life. Sequencing is carried out around the globe and the data is submitted to the public repositories of the International Nucleotide Sequence Database Collaboration. However, the context in which these studies are conducted often gets lost, because experimental data, as well as information about the environment are rarely submitted along with the sequence data. If these contextual or metadata are missing, key opportunities of comparison and analysis across studies and habitats are hampered or even impossible. To address this problem, the Genomic Standards Consortium (GSC) promotes checklists and standards to better describe our sequence data collection and to promote the capturing, exchange and integration of sequence data with contextual data. In a recent community effort the GSC has developed a series of recommendations for contextual data that should be submitted along with sequence data. To support the scientific community to significantly enhance the quality and quantity of contextual data in the public sequence data repositories, specialized software tools are needed. In this work we present CDinFusion, a web-based tool to integrate contextual and sequence data in (Multi)FASTA format prior to submission. The tool is open source and available under the Lesser GNU Public License 3. A public installation is hosted and maintained at the Max Planck Institute for Marine Microbiology at http://www.megx.net/cdinfusion. The tool may also be installed locally using the open source code available at http://code.google.com/p/cdinfusion. PMID:21935468

Characterization of GM events by insert knowledge adapted re-sequencing approaches

PubMed Central

Yang, Litao; Wang, Congmao; Holst-Jensen, Arne; Morisset, Dany; Lin, Yongjun; Zhang, Dabing

2013-01-01

Detection methods and data from molecular characterization of genetically modified (GM) events are needed by stakeholders of public risk assessors and regulators. Generally, the molecular characteristics of GM events are incomprehensively revealed by current approaches and biased towards detecting transformation vector derived sequences. GM events are classified based on available knowledge of the sequences of vectors and inserts (insert knowledge). Herein we present three insert knowledge-adapted approaches for characterization GM events (TT51-1 and T1c-19 rice as examples) based on paired-end re-sequencing with the advantages of comprehensiveness, accuracy, and automation. The comprehensive molecular characteristics of two rice events were revealed with additional unintended insertions comparing with the results from PCR and Southern blotting. Comprehensive transgene characterization of TT51-1 and T1c-19 is shown to be independent of a priori knowledge of the insert and vector sequences employing the developed approaches. This provides an opportunity to identify and characterize also unknown GM events. PMID:24088728

Characterization of GM events by insert knowledge adapted re-sequencing approaches.

PubMed

Yang, Litao; Wang, Congmao; Holst-Jensen, Arne; Morisset, Dany; Lin, Yongjun; Zhang, Dabing

2013-10-03

Detection methods and data from molecular characterization of genetically modified (GM) events are needed by stakeholders of public risk assessors and regulators. Generally, the molecular characteristics of GM events are incomprehensively revealed by current approaches and biased towards detecting transformation vector derived sequences. GM events are classified based on available knowledge of the sequences of vectors and inserts (insert knowledge). Herein we present three insert knowledge-adapted approaches for characterization GM events (TT51-1 and T1c-19 rice as examples) based on paired-end re-sequencing with the advantages of comprehensiveness, accuracy, and automation. The comprehensive molecular characteristics of two rice events were revealed with additional unintended insertions comparing with the results from PCR and Southern blotting. Comprehensive transgene characterization of TT51-1 and T1c-19 is shown to be independent of a priori knowledge of the insert and vector sequences employing the developed approaches. This provides an opportunity to identify and characterize also unknown GM events.

Genome-wide characterization and selection of expressed sequence tag simple sequence repeat primers for optimized marker distribution and reliability in peach

USDA-ARS?s Scientific Manuscript database

Expressed sequence tag (EST) simple sequence repeats (SSRs) in Prunus were mined, and flanking primers designed and used for genome-wide characterization and selection of primers to optimize marker distribution and reliability. A total of 12,618 contigs were assembled from 84,727 ESTs, along with 34...

RECOVIR Software for Identifying Viruses

NASA Technical Reports Server (NTRS)

Chakravarty, Sugoto; Fox, George E.; Zhu, Dianhui

2013-01-01

Most single-stranded RNA (ssRNA) viruses mutate rapidly to generate a large number of strains with highly divergent capsid sequences. Determining the capsid residues or nucleotides that uniquely characterize these strains is critical in understanding the strain diversity of these viruses. RECOVIR (an acronym for "recognize viruses") software predicts the strains of some ssRNA viruses from their limited sequence data. Novel phylogenetic-tree-based databases of protein or nucleic acid residues that uniquely characterize these virus strains are created. Strains of input virus sequences (partial or complete) are predicted through residue-wise comparisons with the databases. RECOVIR uses unique characterizing residues to identify automatically strains of partial or complete capsid sequences of picorna and caliciviruses, two of the most highly diverse ssRNA virus families. Partition-wise comparisons of the database residues with the corresponding residues of more than 300 complete and partial sequences of these viruses resulted in correct strain identification for all of these sequences. This study shows the feasibility of creating databases of hitherto unknown residues uniquely characterizing the capsid sequences of two of the most highly divergent ssRNA virus families. These databases enable automated strain identification from partial or complete capsid sequences of these human and animal pathogens.

Toward the Language-Ready Brain: Biological Evolution and Primate Comparisons.

PubMed

Arbib, Michael A

2017-02-01

The approach to language evolution suggested here focuses on three questions: How did the human brain evolve so that humans can develop, use, and acquire languages? How can the evolutionary quest be informed by studying brain, behavior, and social interaction in monkeys, apes, and humans? How can computational modeling advance these studies? I hypothesize that the brain is language ready in that the earliest humans had protolanguages but not languages (i.e., communication systems endowed with rich and open-ended lexicons and grammars supporting a compositional semantics), and that it took cultural evolution to yield societies (a cultural constructed niche) in which language-ready brains could become language-using brains. The mirror system hypothesis is a well-developed example of this approach, but I offer it here not as a closed theory but as an evolving framework for the development and analysis of conflicting subhypotheses in the hope of their eventual integration. I also stress that computational modeling helps us understand the evolving role of mirror neurons, not in and of themselves, but only in their interaction with systems "beyond the mirror." Because a theory of evolution needs a clear characterization of what it is that evolved, I also outline ideas for research in neurolinguistics to complement studies of the evolution of the language-ready brain. A clear challenge is to go beyond models of speech comprehension to include sign language and models of production, and to link language to visuomotor interaction with the physical and social world.

Development of the PRE-HIT instrument: patient readiness to engage in health information technology.

PubMed

Koopman, Richelle J; Petroski, Gregory F; Canfield, Shannon M; Stuppy, Julie A; Mehr, David R

2014-01-28

Technology-based aids for lifestyle change are becoming more prevalent for chronic conditions. Important "digital divides" remain, as well as concerns about privacy, data security, and lack of motivation. Researchers need a way to characterize participants' readiness to use health technologies. To address this need, we created an instrument to measure patient readiness to engage with health technologies among adult patients with chronic conditions. Initial focus groups to determine domains, followed by item development and refinement, and exploratory factor analysis to determine final items and factor structure. The development sample included 200 patients with chronic conditions from 6 family medicine clinics. From 98 potential items, 53 best candidate items were examined using exploratory factor analysis. Pearson's Correlation for Test/Retest reliability at 3 months. The final instrument had 28 items that sorted into 8 factors with associated Cronbach's alpha: 1) Health Information Need (0.84), 2) Computer/Internet Experience (0.87), 3) Computer Anxiety (0.82), 4) Preferred Mode of Interaction (0.73), 5) Relationship with Doctor (0.65), 6) Cell Phone Expertise (0.75), 7) Internet Privacy (0.71), and 8) No News is Good News (0.57). Test-retest reliability for the 8 subscales ranged from (0.60 to 0.85). The Patient Readiness to Engage in Health Internet Technology (PRE-HIT) instrument has good psychometric properties and will be an aid to researchers investigating technology-based health interventions. Future work will examine predictive validity.

Development of the PRE-HIT instrument: patient readiness to engage in health information technology

PubMed Central

2014-01-01

Background Technology-based aids for lifestyle change are becoming more prevalent for chronic conditions. Important “digital divides” remain, as well as concerns about privacy, data security, and lack of motivation. Researchers need a way to characterize participants’ readiness to use health technologies. To address this need, we created an instrument to measure patient readiness to engage with health technologies among adult patients with chronic conditions. Methods Initial focus groups to determine domains, followed by item development and refinement, and exploratory factor analysis to determine final items and factor structure. The development sample included 200 patients with chronic conditions from 6 family medicine clinics. From 98 potential items, 53 best candidate items were examined using exploratory factor analysis. Pearson’s Correlation for Test/Retest reliability at 3 months. Results The final instrument had 28 items that sorted into 8 factors with associated Cronbach’s alpha: 1) Health Information Need (0.84), 2) Computer/Internet Experience (0.87), 3) Computer Anxiety (0.82), 4) Preferred Mode of Interaction (0.73), 5) Relationship with Doctor (0.65), 6) Cell Phone Expertise (0.75), 7) Internet Privacy (0.71), and 8) No News is Good News (0.57). Test-retest reliability for the 8 subscales ranged from (0.60 to 0.85). Conclusion The Patient Readiness to Engage in Health Internet Technology (PRE-HIT) instrument has good psychometric properties and will be an aid to researchers investigating technology-based health interventions. Future work will examine predictive validity. PMID:24472182

RapTOR: Automated Sequencing Library Preparation and Suppression for Rapid Pathogen Characterization (7th Annual SFAF Meeting, 2012)

ScienceCinema

Lane, Todd

2018-05-18

Todd Lane on "RapTOR: Automated sequencing library preparation and suppression for rapid pathogen characterization" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

RapTOR: Automated Sequencing Library Preparation and Suppression for Rapid Pathogen Characterization (7th Annual SFAF Meeting, 2012)

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

Lane, Todd

2012-06-01

Todd Lane on "RapTOR: Automated sequencing library preparation and suppression for rapid pathogen characterization" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

Characterization of Satellite DNA Sequences from the Commercially Important Marine Rotifers Brachionus rotundiformis and Brachionus plicatilis.

PubMed

Boehm; Gibson; Lubzens

2000-01-01

This study was initiated to search for species-specific and strain-specific satellite DNA sequences for which oligonucleotide primers could be designed to differentiate between various commercially important strains of the marine monogonont rotifers Brachionus rotundiformis and Brachionus plicatilis. Two unrelated, highly reiterated satellite sequences were cloned and characterized. The eight sequenced monomers from B. rotundiformis and six from B. plicatilis had low intrarepeat variability and were similar in their overall lengths, A + T compositions, and high degrees of repeated motif substructure. However, hybridizations to 19 representative strains, sequence characterizations, and GenBank searches indicated that these two satellites are morphotype-specific and population-specific, respectively, and share little homology to each other or to other characterized sequences in the database. Primer pairs designed for the B. rotundiformis satellite confirmed hybridization specificities on polymerase chain reaction and could serve as a useful molecular diagnostic tool to identify strains belonging to the SS morphotype, which are gaining widespread usage as first feeds for marine fish in commercial production.

Enhanced arbovirus surveillance with deep sequencing: Identification of novel rhabdoviruses and bunyaviruses in Australian mosquitoes.

PubMed

Coffey, Lark L; Page, Brady L; Greninger, Alexander L; Herring, Belinda L; Russell, Richard C; Doggett, Stephen L; Haniotis, John; Wang, Chunlin; Deng, Xutao; Delwart, Eric L

2014-01-05

Viral metagenomics characterizes known and identifies unknown viruses based on sequence similarities to any previously sequenced viral genomes. A metagenomics approach was used to identify virus sequences in Australian mosquitoes causing cytopathic effects in inoculated mammalian cell cultures. Sequence comparisons revealed strains of Liao Ning virus (Reovirus, Seadornavirus), previously detected only in China, livestock-infecting Stretch Lagoon virus (Reovirus, Orbivirus), two novel dimarhabdoviruses, named Beaumont and North Creek viruses, and two novel orthobunyaviruses, named Murrumbidgee and Salt Ash viruses. The novel virus proteomes diverged by ≥ 50% relative to their closest previously genetically characterized viral relatives. Deep sequencing also generated genomes of Warrego and Wallal viruses, orbiviruses linked to kangaroo blindness, whose genomes had not been fully characterized. This study highlights viral metagenomics in concert with traditional arbovirus surveillance to characterize known and new arboviruses in field-collected mosquitoes. Follow-up epidemiological studies are required to determine whether the novel viruses infect humans. © 2013 Elsevier Inc. All rights reserved.

Genome-wide characterization of centromeric satellites from multiple mammalian genomes.

PubMed

Alkan, Can; Cardone, Maria Francesca; Catacchio, Claudia Rita; Antonacci, Francesca; O'Brien, Stephen J; Ryder, Oliver A; Purgato, Stefania; Zoli, Monica; Della Valle, Giuliano; Eichler, Evan E; Ventura, Mario

2011-01-01

Despite its importance in cell biology and evolution, the centromere has remained the final frontier in genome assembly and annotation due to its complex repeat structure. However, isolation and characterization of the centromeric repeats from newly sequenced species are necessary for a complete understanding of genome evolution and function. In recent years, various genomes have been sequenced, but the characterization of the corresponding centromeric DNA has lagged behind. Here, we present a computational method (RepeatNet) to systematically identify higher-order repeat structures from unassembled whole-genome shotgun sequence and test whether these sequence elements correspond to functional centromeric sequences. We analyzed genome datasets from six species of mammals representing the diversity of the mammalian lineage, namely, horse, dog, elephant, armadillo, opossum, and platypus. We define candidate monomer satellite repeats and demonstrate centromeric localization for five of the six genomes. Our analysis revealed the greatest diversity of centromeric sequences in horse and dog in contrast to elephant and armadillo, which showed high-centromeric sequence homogeneity. We could not isolate centromeric sequences within the platypus genome, suggesting that centromeres in platypus are not enriched in satellite DNA. Our method can be applied to the characterization of thousands of other vertebrate genomes anticipated for sequencing in the near future, providing an important tool for annotation of centromeres.

e-Health readiness assessment factors and measuring tools: A systematic review.

PubMed

Yusif, Salifu; Hafeez-Baig, Abdul; Soar, Jeffrey

2017-11-01

The evolving, adoption and high failure nature of health information technology (HIT)/IS/T systems requires effective readiness assessment to avert increasing failures while increasing system benefits. However, literature on HIT readiness assessment is myriad and fragmented. This review bares the contours of the available literature concluding in a set of manageable and usable recommendations for policymakers, researchers, individuals and organizations intending to assess readiness for any HIT implementation. Identify studies, analyze readiness factors and offer recommendations. Published articles 1995-2016 were searched using Medline/PubMed, Cinahl, Web of Science, PsychInfo, ProQuest. Studies were included if they were assessing IS/T/mHealth readiness in the context of HIT. Articles not written in English were excluded. Themes that emerged in the process of the data synthesis were thematically analysed and interpreted. Analyzed themes were found across 63 articles. In accordance with their prevalence of use, they included but not limited to "Technological readiness", 30 (46%); "Core/Need/Motivational readiness", 23 (37%); "Acceptance and use readiness", 19 (29%); "Organizational readiness", 20 (21%); "IT skills/Training/Learning readiness" (18%), "Engagement readiness", 16 (24%) and "Societal readiness" (14%). Despite their prevalence in use, "Technological readiness", "Motivational readiness" and "Engagement readiness" all had myriad and unreliable measuring tools. Core readiness had relatively reliable measuring tools, which repeatedly been used in various readiness assessment studies CONCLUSION: Thus, there is the need for reliable measuring tools for even the most commonly used readiness assessment factors/constructs: Core readiness, Engagement and buy-ins readiness, Technological readiness and IT Skills readiness as this could serve as an immediate step in conducting effective/reliable e-Health readiness assessment, which could lead to reduced HIT implementation failures. Copyright © 2017 Elsevier B.V. All rights reserved.

CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences

PubMed Central

2012-01-01

Background The complete sequences of chloroplast genomes provide wealthy information regarding the evolutionary history of species. With the advance of next-generation sequencing technology, the number of completely sequenced chloroplast genomes is expected to increase exponentially, powerful computational tools annotating the genome sequences are in urgent need. Results We have developed a web server CPGAVAS. The server accepts a complete chloroplast genome sequence as input. First, it predicts protein-coding and rRNA genes based on the identification and mapping of the most similar, full-length protein, cDNA and rRNA sequences by integrating results from Blastx, Blastn, protein2genome and est2genome programs. Second, tRNA genes and inverted repeats (IR) are identified using tRNAscan, ARAGORN and vmatch respectively. Third, it calculates the summary statistics for the annotated genome. Fourth, it generates a circular map ready for publication. Fifth, it can create a Sequin file for GenBank submission. Last, it allows the extractions of protein and mRNA sequences for given list of genes and species. The annotation results in GFF3 format can be edited using any compatible annotation editing tools. The edited annotations can then be uploaded to CPGAVAS for update and re-analyses repeatedly. Using known chloroplast genome sequences as test set, we show that CPGAVAS performs comparably to another application DOGMA, while having several superior functionalities. Conclusions CPGAVAS allows the semi-automatic and complete annotation of a chloroplast genome sequence, and the visualization, editing and analysis of the annotation results. It will become an indispensible tool for researchers studying chloroplast genomes. The software is freely accessible from http://www.herbalgenomics.org/cpgavas. PMID:23256920

76 FR 66891 - Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-28

... Respondents: 265. Average Hours per Response: StormReady, Tsunami-Ready and StormReady/TsunamiReady... request is for revision of a current information collection. The StormReady, TsunamiReady and and StormReady/TsunamiReady Programs are voluntary programs offered to provide guidance and incentive to...

The Preparation and Characterization of the Geometric Isomers of a Coordination Complex: cis- and trans-bis Glycinato Copper (II) Monohydrates.

ERIC Educational Resources Information Center

O'Brien, Paul

1982-01-01

Preparation of cis and trans isomers of the kinetically labile bis glycinato copper (II) has a number of advantages including its facility, economy, ready theoretical interpretation, and biological relevance. Background information, laboratory procedures, results/discussion are provided for this experiment which can be completed in a single,…

Getting Ready for School: Palm Beach County's Early Childhood Cluster Initiative. Executive Summary

ERIC Educational Resources Information Center

Spielberger, Julie; Baker, Stephen; Winje, Carolyn

2008-01-01

This report summarizes findings from the second year of an implementation study of the Early Childhood Cluster Initiative (ECCI). ECCI is a prekindergarten program in ten elementary schools and a community child care center in Palm Beach County, based on the design of the High/Scope Perry Preschool model. The initiative is characterized by low…

Defense Research Enterprise Assessment

DTIC Science & Technology

2017-01-01

ACQUISITION, TECHNOLOGY , AND LOGISTICS OFFICE OF THE UNDER SECRETARY OF DEFENSE 3000 DEFENSE PENTAGON WASHINGTON, DC 20301-3000 JAN 2 5 2017...fulfill vital missions on behalf of the Warfighter. This DoD research enterprise is characterized by high-quality science, technology transition, and...smart acquisition. The rapidly changing technology landscape means that the Labs also must adapt their mission to continue to serve and ready

Characterization of Microbial Population Structures in Recreational Waters and Primary Sources of Fecal Pollution with a Next-Generation Sequencing Approach

EPA Science Inventory

The invention of new approaches to DNA sequencing commonly referred to as next generation sequencing technologies is revolutionizing the study of microbial diversity. In this chapter, we discuss the characterization of microbial population structures in recreational waters and p...

Characterization of the ecological interactions of Roundup Ready 2 Yield® soybean, MON 89788, for use in ecological risk assessment

PubMed Central

Horak, Michael J; Rosenbaum, Eric W; Phillips, Samuel L; Kendrick, Daniel L; Carson, David; Clark, Pete L; Nickson, Thomas E

2015-01-01

Abstract As part of an ecological risk assessment, Roundup Ready 2 Yield® soybean (MON 89788) was compared to a conventional control soybean variety, A3244, for disease and arthropod damage, plant response to abiotic stress and cold, effects on succeeding plant growth (allelopathic effects), plant response to a bacterial symbiont, and effects on the ability of seed to survive and volunteer in a subsequent growing season. Statistically significant differences between MON 89788 and A3244 were considered in the context of the genetic variation known to occur in soybean and were assessed for their potential impact on plant pest (weed) potential and adverse environmental impact. The results of these studies revealed no effects of the genetic modification that would result in increased pest potential or adverse environmental impact of MON 89788 compared with A3244. This paper illustrates how such characterization studies conducted in a range of environments where the crop is grown are used in an ecological risk assessment of the genetically modified (GM) crop. Furthermore, risk assessors and decision makers use this information when deciding whether to approve a GM crop for cultivation in—or grain import into—their country. PMID:26177011

How well do TTM measures work among a sample of individuals with unhealthy alcohol use that is characterized by low readiness to change?

PubMed

Baumann, Sophie; Gaertner, Beate; Schnuerer, Inga; Bischof, Gallus; John, Ulrich; Freyer-Adam, Jennis

2013-09-01

Little is known about the applicability of the transtheoretical model of intentional behavior change (TTM) to individuals with unhealthy alcohol use that is primarily characterized by low readiness to change. This study examined the psychometric properties of short measures by assessing three core constructs of the TTM: the 20-item Processes of Change (POC-20) scale, and short versions of the Alcohol Decisional Balance Scale (ADBS) and the Alcohol Abstinence Self-Efficacy (AASE) scale. A sample of 427 individuals with unhealthy alcohol use (Mage = 30 years, 65% men), identified at job agencies in northeastern Germany, completed all three scales. Item difficulty (d), selectivity (rit), and Cronbach's alpha were calculated. Confirmatory factory analyses were used to test for construct validity and latent mean differences across the stages. The psychometric properties of the 8-item AASE were adequate (d range: 0.59-0.78; rit range: 0.59-0.68; α range: 0.74-0.81), except for one subscale. Most items of the POC-20 and the 10-item ADBS were difficult (dPOC range: 0.08-0.40; dADBS range: 0.21-0.58); selectivity (ritPOC range: 0.26-0.62; ritADBS range: 0.34-0.68) and internal consistency (αPOC range: 0.41-0.76; αADBS range: 0.64-0.78) were low to moderate. Construct validity was acceptable (Comparative Fit Index range: 0.95-0.99). The association between stages and TTM constructs partially followed expected patterns. Suggestions for modifications of TTM measures are discussed for better applicability among proactively recruited samples of individuals with unhealthy alcohol use and with primarily low readiness to change. (PsycINFO Database Record (c) 2013 APA, all rights reserved).

Prevalence and molecular characterization of Clostridium difficile isolates from a pig slaughterhouse, pork, and humans in Taiwan.

PubMed

Wu, Ying-Chen; Chen, Chih-Ming; Kuo, Chih-Jung; Lee, Jen-Jie; Chen, Pin-Chun; Chang, Yi-Chih; Chen, Ter-Hsin

2017-02-02

Clostridium difficile causes antibiotic-associated diarrhea in both humans and animals. The ribotype 078, predominant in food animals, is associated with community-acquired C. difficile infection, and C. difficile is suggested to be a foodborne pathogen. Recently, the C. difficile ribotype 078 lineage emerged in patients and pigs in Taiwan. This study aimed to investigate the prevalence and molecular characterization of C. difficile isolated from a pig slaughterhouse, retail meat, ready-to-eat meals, and humans in Taiwan. We collected samples from one slaughterhouse (n=422), 29 retail markets (raw pork, n=62; ready-to-eat pork, n=65), and one hospital (non-diarrheal humans, stool, n=317) in 2015. The isolated C. difficile were subjected to ribotyping and multilocus variable-number tandem-repeat analysis (MLVA). In the slaughterhouse, the isolation rate from carcasses was high (23%, 21/92) and ribotype 126 dominated. Scalding water was found to have C. difficile contamination (44%, 4/9), and two of the seven isolates were ribotype 126. The isolation rates from raw pork and ready-to-eat pork were between 20% and 29%. Ribotypes 126, 127, and 014 were found in raw pork, whereas ribotype 078 was not identified in this study. Eight isolates-seven non-toxigenic isolates and one ribotype 017-were found in non-diarrheal human samples. Notably, MLVA showed that ribotype 126 isolates from the slaughterhouse, pig stool, colons, carcasses, and scalding water were closely genetically related, indicating serious risk for cross-contamination. However, the genetic evidence of foodborne transmission from carcasses to food and humans is still lacking. Copyright © 2016. Published by Elsevier B.V.

Cigarette Purchasing Patterns, Readiness to Quit, and Quit Attempts Among Homeless Smokers.

PubMed

Wrighting, Quentaxia; Businelle, Michael S; Kendzor, Darla E; LeBlanc, Hannah; Reitzel, Lorraine R

2017-11-07

Cigarette purchasing patterns may be linked with greater readiness to make a quit attempt and more quit attempts among domiciled samples. However, little is known about the cigarette purchasing patterns of homeless smokers or their potential relations to quitting intention and behaviors. This study redressed this gap among a convenience sample of homeless adult smokers from a large shelter in Dallas, Texas. Participants (N = 207; Mage = 43; 71.5% male) smoked ≥100 cigarettes over the lifetime and endorsed current daily smoking. Variables assessed included cigarette dependence (time to first cigarette of the day), monthly income, quantity of cigarettes most recently purchased, average money spent on cigarettes weekly, readiness/motivation to quit smoking, and the number intentional quit attempts lasting ≥24h in the past year. Regression analyses were conducted to characterize associations of cigarette purchasing patterns with readiness to quit and quit attempts controlling for sex, age, cigarette dependence, and income. Most participants purchased cigarettes by the pack (61.4%), and more than half the sample spent ≤$20 on cigarettes per week. Results indicated that spending less money per week on cigarettes was associated with greater readiness to quit (P = .016), even when controlling for income, cigarette dependence, and other covariates. Stratified analyses indicated that this association was significant only for homeless smokers reporting no regular monthly income. Homeless daily smokers with no reported income who spend little money on cigarettes may make particularly apt targets for cessation interventions due to potential associations with quitting motivation. Adults who are homeless smoke at greater rates and quit at lower rates than domiciled adults, leading to significant smoking-related health disparities among this group. Findings suggest that cigarette purchasing patterns are linked with readiness to quit smoking among smokers who are homeless. Results elucidate one of the myriad factors that contribute to tobacco-related disparities among this group and findings may have implications for cessation interventions in homeless shelters and other contexts where resources are limited. © The Author 2016. Published by Oxford University Press on behalf of the Society for Research on Nicotine and Tobacco. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Isolation of an insertion sequence (IS1051) from Xanthomonas campestris pv. dieffenbachiae with potential use for strain identification and characterization.

PubMed Central

Berthier, Y; Thierry, D; Lemattre, M; Guesdon, J L

1994-01-01

A new insertion sequence was isolated from Xanthomonas campestris pv. dieffenbachiae. Sequence analysis showed that this element is 1,158 bp long and has 15-bp inverted repeat ends containing two mismatches. Comparison of this sequence with sequences in data bases revealed significant homology with Escherichia coli IS5. IS1051, which detected multiple restriction fragment length polymorphisms, was used as a probe to characterize strains from the pathovar dieffenbachiae. Images PMID:7906933

KSC-2009-6236

NASA Image and Video Library

2009-11-09

CAPE CANAVERAL, Fla. – At the Astrotech Space Operations facility in Titusville, Fla., the Solar Dynamics Observatory, or SDO, with its solar arrays deployed, is ready to receive signal commands to test the release mechanism sequence for the arrays. SDO is the first space weather research network mission in NASA's Living With a Star Program. The spacecraft's long-term measurements will give solar scientists in-depth information about changes in the sun's magnetic field and insight into how they affect Earth. Liftoff on an Atlas V rocket is scheduled for Feb. 3, 2010. Photo credit: NASA/Jack Pfaller

Polyunsaturated C-Glycosidic 4-Hydroxy-2-pyrone Derivatives: Total Synthesis Shows that Putative Orevactaene Is Likely Identical with Epipyrone A.

PubMed

Preindl, Johannes; Schulthoff, Saskia; Wirtz, Conny; Lingnau, Julia; Fürstner, Alois

2017-06-19

Orevactaene and epipyrone A were previously thought to comprise the same polyunsaturated tail but notably different C-glycosylated 4-hydroxy-2-pyrone head groups. Total synthesis now shows that the signature bicyclic framework assigned to orevactaene is a chimera; the compound is almost certainly identical with epipyrone A, whose previously unknown stereochemistry has also been established during this study. Key to success was the ready formation of the bicyclic core of putative orevactaene by a sequence of two alkyne cycloisomerization reactions using tungsten and gold catalysis. Equally important was the flexibility in the assembly process gained by the use of heterobimetallic polyunsaturated modules whose termini could be selectively and consecutively addressed in a practical one-pot cross-coupling sequence. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Real-Time PCR-Based Quantitation Method for the Genetically Modified Soybean Line GTS 40-3-2.

PubMed

Kitta, Kazumi; Takabatake, Reona; Mano, Junichi

2016-01-01

This chapter describes a real-time PCR-based method for quantitation of the relative amount of genetically modified (GM) soybean line GTS 40-3-2 [Roundup Ready(®) soybean (RRS)] contained in a batch. The method targets a taxon-specific soybean gene (lectin gene, Le1) and the specific DNA construct junction region between the Petunia hybrida chloroplast transit peptide sequence and the Agrobacterium 5-enolpyruvylshikimate-3-phosphate synthase gene (epsps) sequence present in GTS 40-3-2. The method employs plasmid pMulSL2 as a reference material in order to quantify the relative amount of GTS 40-3-2 in soybean samples using a conversion factor (Cf) equal to the ratio of the RRS-specific DNA to the taxon-specific DNA in representative genuine GTS 40-3-2 seeds.

A bioinformatics approach for identifying transgene insertion sites using whole genome sequencing data.

PubMed

Park, Doori; Park, Su-Hyun; Ban, Yong Wook; Kim, Youn Shic; Park, Kyoung-Cheul; Kim, Nam-Soo; Kim, Ju-Kon; Choi, Ik-Young

2017-08-15

Genetically modified crops (GM crops) have been developed to improve the agricultural traits of modern crop cultivars. Safety assessments of GM crops are of paramount importance in research at developmental stages and before releasing transgenic plants into the marketplace. Sequencing technology is developing rapidly, with higher output and labor efficiencies, and will eventually replace existing methods for the molecular characterization of genetically modified organisms. To detect the transgenic insertion locations in the three GM rice gnomes, Illumina sequencing reads are mapped and classified to the rice genome and plasmid sequence. The both mapped reads are classified to characterize the junction site between plant and transgene sequence by sequence alignment. Herein, we present a next generation sequencing (NGS)-based molecular characterization method, using transgenic rice plants SNU-Bt9-5, SNU-Bt9-30, and SNU-Bt9-109. Specifically, using bioinformatics tools, we detected the precise insertion locations and copy numbers of transfer DNA, genetic rearrangements, and the absence of backbone sequences, which were equivalent to results obtained from Southern blot analyses. NGS methods have been suggested as an effective means of characterizing and detecting transgenic insertion locations in genomes. Our results demonstrate the use of a combination of NGS technology and bioinformatics approaches that offers cost- and time-effective methods for assessing the safety of transgenic plants.

Molecular Characterization of Transgene Integration by Next-Generation Sequencing in Transgenic Cattle

PubMed Central

Zhang, Ran; Yin, Yinliang; Zhang, Yujun; Li, Kexin; Zhu, Hongxia; Gong, Qin; Wang, Jianwu; Hu, Xiaoxiang; Li, Ning

2012-01-01

As the number of transgenic livestock increases, reliable detection and molecular characterization of transgene integration sites and copy number are crucial not only for interpreting the relationship between the integration site and the specific phenotype but also for commercial and economic demands. However, the ability of conventional PCR techniques to detect incomplete and multiple integration events is limited, making it technically challenging to characterize transgenes. Next-generation sequencing has enabled cost-effective, routine and widespread high-throughput genomic analysis. Here, we demonstrate the use of next-generation sequencing to extensively characterize cattle harboring a 150-kb human lactoferrin transgene that was initially analyzed by chromosome walking without success. Using this approach, the sites upstream and downstream of the target gene integration site in the host genome were identified at the single nucleotide level. The sequencing result was verified by event-specific PCR for the integration sites and FISH for the chromosomal location. Sequencing depth analysis revealed that multiple copies of the incomplete target gene and the vector backbone were present in the host genome. Upon integration, complex recombination was also observed between the target gene and the vector backbone. These findings indicate that next-generation sequencing is a reliable and accurate approach for the molecular characterization of the transgene sequence, integration sites and copy number in transgenic species. PMID:23185606

Analysis and Visualization of ChIP-Seq and RNA-Seq Sequence Alignments Using ngs.plot.

PubMed

Loh, Yong-Hwee Eddie; Shen, Li

2016-01-01

The continual maturation and increasing applications of next-generation sequencing technology in scientific research have yielded ever-increasing amounts of data that need to be effectively and efficiently analyzed and innovatively mined for new biological insights. We have developed ngs.plot-a quick and easy-to-use bioinformatics tool that performs visualizations of the spatial relationships between sequencing alignment enrichment and specific genomic features or regions. More importantly, ngs.plot is customizable beyond the use of standard genomic feature databases to allow the analysis and visualization of user-specified regions of interest generated by the user's own hypotheses. In this protocol, we demonstrate and explain the use of ngs.plot using command line executions, as well as a web-based workflow on the Galaxy framework. We replicate the underlying commands used in the analysis of a true biological dataset that we had reported and published earlier and demonstrate how ngs.plot can easily generate publication-ready figures. With ngs.plot, users would be able to efficiently and innovatively mine their own datasets without having to be involved in the technical aspects of sequence coverage calculations and genomic databases.

Genetic characterization of uncultured fungal endophytes from Bouteloua eriopoda and Atriplex canescens

Treesearch

Mary E. Lucero; Jerry R. Barrow; Ruth Sedillo; Pedro Osuna-Avila; Isaac Reyes-Vera

2008-01-01

Obligate fungal endophytes form cryptic communities in vascular plants that can defy detection and isolation by microscopic examination of reproductive structures. Molecular detection by PCR amplification of fungal DNA sequences alone is insufficient, since target endophyte sequences are unknown and difficult to distinguish from sequences already characterized as plant...

Laboratory results of the AOF system testing

NASA Astrophysics Data System (ADS)

Kolb, Johann; Madec, Pierre-Yves; Arsenault, Robin; Oberti, Sylvain; Paufique, Jérôme; La Penna, Paolo; Ströbele, Stefan; Donaldson, Robert; Soenke, Christian; Suárez Valles, Marcos; Kiekebusch, Mario; Argomedo, Javier; Le Louarn, Miska; Vernet, Elise; Haguenauer, Pierre; Duhoux, Philippe; Aller-Carpentier, Emmanuel; Valenzuela, Jose Javier; Guerra, Juan Carlos

2016-07-01

For two years starting in February 2014, the AO modules GRAAL for HAWK-I and GALACSI for MUSE of the Adaptive Optics Facility project have undergone System Testing at ESO's Headquarters. They offer four different modes: NGS SCAO, LGS GLAO in the IR, LGS GLAO and LTAO in the visible. A detailed characterization of those modes was made possible by the existence of ASSIST, a test bench emulating an adaptive VLT including the Deformable Secondary Mirror, a star simulator and turbulence generator and a VLT focal plane re-imager. This phase aimed at validating all the possible components and loops of the AO modules before installation at the actual VLT that comprises the added complexity of real LGSs, a harsher non-reproducible environment and the adaptive telescope control. In this paper we present some of the major results obtained and challenges encountered during the phase of System Tests, like the preparation of the Acquisition sequence, the testing of the Jitter loop, the performance optimization in GLAO and the offload of low-order modes from the DSM to the telescope (restricted to the M2 hexapod). The System Tests concluded with the successful acceptance, shipping, installation and first commissioning of GRAAL in 2015 as well as the acceptance and shipping of GALACSI, ready for installation and commissioning early 2017.

Ex-vivo imaging of blood and lymphatic vessels in conjunctiva using optical coherence tomography

NASA Astrophysics Data System (ADS)

Gong, Peijun; Karnowski, Karol; Yu, Paula; An, Dong; Yu, Dao-Yi; Sampson, David D.

2017-04-01

Label-free imaging of the blood and lymphatic vessel networks of the conjunctiva of the eye is important in assessing the drainage pathways affected by glaucoma. We utilize the characteristically low signal in optical coherence tomography (OCT) provided by such vessels in ex vivo tissue to characterize their morphology in two and three dimensions. We demonstrate this method on conjunctiva from six porcine eyes, showing the ready visualization of both vessel networks. Such ex vivo characterization is a necessary precursor for future in vivo studies directed towards improving glaucoma surgery.

AVTA Federal Fleet PEV Readiness Data Logging and Characterization Study for Department of Veterans Affairs. James J. Peters VA Medical Center, Bronx, NY

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

Schey, Stephen; Francfort, Jim

This report focuses on the Department of Veterans Affairs, James J. Peters VA Medical Center (VA - Bronx) fleet to identify daily operational characteristics of select vehicles and report findings on vehicle and mission characterizations to support the successful introduction of PEVs into the agencies’ fleets. Individual observations of these selected vehicles provide the basis for recommendations related to electric vehicle adoption and whether a battery electric vehicle or plug-in hybrid electric vehicle (collectively referred to as PEVs) can fulfill the mission requirements.

AVTA Federal Fleet PEV Readiness Data Logging and Characterization Study for the National Park Service: Sleeping Bear Dunes National Lakeshore

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

Schey, Stephen; Francfort, Jim

This report focuses on the Sleeping Bear Dunes National Lakeshore (SLBE) fleet to identify daily operational characteristics of select vehicles and report findings on vehicle and mission characterizations to support the successful introduction of plug-in electric vehicles (PEVs) into the agencies’ fleets. Individual observations of these selected vehicles provide the basis for recommendations related to electric vehicle adoption and whether a battery electric vehicle (BEV) or plug-in hybrid electric vehicle (PHEV) (collectively plug-in electric vehicles, or PEVs) can fulfill the mission requirements.

Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products.

PubMed

Holst-Jensen, Arne; Spilsberg, Bjørn; Arulandhu, Alfred J; Kok, Esther; Shi, Jianxin; Zel, Jana

2016-07-01

The emergence of high-throughput, massive or next-generation sequencing technologies has created a completely new foundation for molecular analyses. Various selective enrichment processes are commonly applied to facilitate detection of predefined (known) targets. Such approaches, however, inevitably introduce a bias and are prone to miss unknown targets. Here we review the application of high-throughput sequencing technologies and the preparation of fit-for-purpose whole genome shotgun sequencing libraries for the detection and characterization of genetically modified and derived products. The potential impact of these new sequencing technologies for the characterization, breeding selection, risk assessment, and traceability of genetically modified organisms and genetically modified products is yet to be fully acknowledged. The published literature is reviewed, and the prospects for future developments and use of the new sequencing technologies for these purposes are discussed.

Characterization and Amplification of Gene-Based Simple Sequence Repeat (SSR) Markers in Date Palm.

PubMed

Zhao, Yongli; Keremane, Manjunath; Prakash, Channapatna S; He, Guohao

2017-01-01

The paucity of molecular markers limits the application of genetic and genomic research in date palm (Phoenix dactylifera L.). Availability of expressed sequence tag (EST) sequences in date palm may provide a good resource for developing gene-based markers. This study characterizes a substantial fraction of transcriptome sequences containing simple sequence repeats (SSRs) from the EST sequences in date palm. The EST sequences studied are mainly homologous to those of Elaeis guineensis and Musa acuminata. A total of 911 gene-based SSR markers, characterized with functional annotations, have provided a useful basis not only for discovering candidate genes and understanding genetic basis of traits of interest but also for developing genetic and genomic tools for molecular research in date palm, such as diversity study, quantitative trait locus (QTL) mapping, and molecular breeding. The procedures of DNA extraction, polymerase chain reaction (PCR) amplification of these gene-based SSR markers, and gel electrophoresis of PCR products are described in this chapter.

Genetic characterization of K13965, a strain of Oak Vale virus from Western Australia

PubMed Central

Quan, Phenix-Lan; Williams, David T.; Johansen, Cheryl A.; Jain, Komal; Petrosov, Alexandra; Diviney, Sinead M.; Tashmukhamedova, Alla; Hutchison, Stephen K.; Tesh, Robert B.; Mackenzie, John S.; Briese, Thomas; Lipkin, W. Ian

2011-01-01

K13965, an uncharacterized virus, was isolated in 1993 from Anopheles annulipes mosquitoes collected in the Kimberley region of northern Western Australia. Here, we report its genomic sequence, identify it as a rhabdovirus, and characterize its phylogenetic relationships. The genome comprises a P′ (C) and SH protein similar to the recently characterized Tupaia and Durham viruses, and shows overlap between G and L genes. Comparison of K13965 genome sequence to other rhabdoviruses identified K13965 as a strain of the unclassified Australian Oak Vale rhabdovirus, whose complete genome sequence we also determined. Phylogenetic analysis of N and L sequences indicated genetic relationship to a recently proposed Sandjima virus clade, although the Oak Vale virus sequences form a branch separate from the African members of that group. PMID:21740935

A ready-to-use duplex qPCR to detect Leishmania infantum DNA in naturally infected dogs.

PubMed

Rampazzo, Rita de Cássia Pontello; Solcà, Manuela da Silva; Santos, Liliane Celestino Sales; Pereira, Lais de Novaes; Guedes, José Carlos Oliveira; Veras, Patrícia Sampaio Tavares; Fraga, Deborah Bittencourt Mothé; Krieger, Marco Aurélio; Costa, Alexandre Dias Tavares

2017-11-15

Canine visceral leishmaniasis (CVL) is a systemic disease caused by Leishmania infantum. A precise CVL diagnosis would allow for a faster and more specific treatment. Quantitative PCR (qPCR) is a sensitive and specific technique that can diagnose CVL and also monitor parasite load in the animal during the course of the infection or treatment. The aim of this study was to develop a ready-to-use (gelified and freezer-free) duplex qPCR for the identification of infected animals. We combined a new qPCR protocol that detects the canine 18S rRNA gene with an existing protocol for L. infantum kDNA detection, creating a duplex qPCR. This duplex method was then developed into a ready-to-use format. The performance of the duplex and singleplex reactions were compared in the traditional format (liquid and freezer-stored). Furthermore, the duplex qPCR performance was compared between the ready-to-use and traditional formats. The singleplex and new duplex qPCR exhibited the same detection limit in the traditional format (0.1 parasites/reaction). The ready-to-use format showed a detection limit of 1 parasite/reaction without affecting the reaction efficiency. The performance of the new qPCR protocol in the two formats was assessed using canine tissue samples from 82 dogs in an endemic CVL area that were previously characterized by standard serological and parasitological protocols. Splenic aspirates provided a higher rate of positivity (92.9%) followed by skin (50%) and blood (35.7%). The reported detection limits were observed for all tissues studied. Our results show that the amplification of L. infantum kDNA and canine DNA in a single tube, using either the traditional or ready-to-use format, exhibited the same diagnostic performance as amplification of the parasite kDNA alone. The detection of the host gene strengthens the qPCR results by confirming the presence and quality of DNA in the samples and the absence of polymerase inhibitors. The ready-to-use duplex qPCR format has many advantages. By joining two qPCR protocols into one, more results can be obtained in the same amount of time with reduced costs and embedded quality control. Reagents are preloaded and stored on the plate, reducing the operator's hands-on time to set up a reaction, as well as decreasing manipulation steps, which reduces the risk of mistakes or contamination. Thus, the ready-to-use duplex format turns qPCR into a robust, easy-to-use tool, which could help increase the availability of qPCR for CVL diagnosis. Copyright © 2017 Elsevier B.V. All rights reserved.

Characterization of three mycoviruses co-infecting the plant pathogenic fungus Sclerotinia nivalis

USDA-ARS?s Scientific Manuscript database

Two dsRNAs of approximately 6.0- and 3.0-kb in length were detected in strain SsSn-1 of Sclerotinia nivalis. Genomic analysis showed that the 6.0-kb dsRNA was a victorivirus, named as Sclerotinia nivalis victorivirus 1 (SnVV1). The genome of SnVV1 is 5162 bp in length containing two large open readi...

High-Temperature Gas-Cooled Test Reactor Point Design

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

Sterbentz, James William; Bayless, Paul David; Nelson, Lee Orville

2016-04-01

A point design has been developed for a 200 MW high-temperature gas-cooled test reactor. The point design concept uses standard prismatic blocks and 15.5% enriched UCO fuel. Reactor physics and thermal-hydraulics simulations have been performed to characterize the capabilities of the design. In addition to the technical data, overviews are provided on the technological readiness level, licensing approach and costs.

Proceedings of the Annual Meeting of the Council for Programs in Technical and Scientific Communication (12th, Oxford, Ohio, February 13-15, 1985).

ERIC Educational Resources Information Center

Samuels, Marilyn Schauer, Ed.

The papers in this proceedings of the Council for Programs in Technical and Scientific Communication (CPTSC) conference discuss collaboration with other disciplines, with business and industry, and with research foundations, reflecting the readiness to reach out that characterizes CPTSC in its second decade. Papers in the proceedings are:…

Multiplex Nucleic Acid Sequence-Based Amplification for Simultaneous Detection of Several Enteric Viruses in Model Ready-To-Eat Foods†

PubMed Central

Jean, Julie; D'Souza, Doris H.; Jaykus, Lee-Ann

2004-01-01

Human enteric viruses are currently recognized as one of the most important causes of food-borne disease. Implication of enteric viruses in food-borne outbreaks can be difficult to confirm due to the inadequacy of the detection methods available. In this study, a nucleic acid sequence-based amplification (NASBA) method was developed in a multiplex format for the specific, simultaneous, and rapid detection of epidemiologically relevant human enteric viruses. Three previously reported primer sets were used in a single reaction for the amplification of RNA target fragments of 474, 371, and 165 nucleotides for the detection of hepatitis A virus and genogroup I and genogroup II noroviruses, respectively. Amplicons were detected by agarose gel electrophoresis and confirmed by electrochemiluminescence and Northern hybridization. Endpoint detection sensitivity for the multiplex NASBA assay was approximately 10−1 reverse transcription-PCR-detectable units (or PFU, as appropriate) per reaction. When representative ready-to-eat foods (deli sliced turkey and lettuce) were inoculated with various concentrations of each virus and processed for virus detection with the multiplex NASBA method, all three human enteric viruses were simultaneously detected at initial inoculum levels of 100 to 102 reverse transcription-PCR-detectable units (or PFU)/9 cm2 in both food commodities. The multiplex NASBA system provides rapid and simultaneous detection of clinically relevant food-borne viruses in a single reaction tube and may be a promising alternative to reverse transcription-PCR for the detection of viral contamination of foods. PMID:15528524

Preparation of Low-Input and Ligation-Free ChIP-seq Libraries Using Template-Switching Technology.

PubMed

Bolduc, Nathalie; Lehman, Alisa P; Farmer, Andrew

2016-10-10

Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) has become the gold standard for mapping of transcription factors and histone modifications throughout the genome. However, for ChIP experiments involving few cells or targeting low-abundance transcription factors, the small amount of DNA recovered makes ligation of adapters very challenging. In this unit, we describe a ChIP-seq workflow that can be applied to small cell numbers, including a robust single-tube and ligation-free method for preparation of sequencing libraries from sub-nanogram amounts of ChIP DNA. An example ChIP protocol is first presented, resulting in selective enrichment of DNA-binding proteins and cross-linked DNA fragments immobilized on beads via an antibody bridge. This is followed by a protocol for fast and easy cross-linking reversal and DNA recovery. Finally, we describe a fast, ligation-free library preparation protocol, featuring DNA SMART technology, resulting in samples ready for Illumina sequencing. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

ALEA: a toolbox for allele-specific epigenomics analysis.

PubMed

Younesy, Hamid; Möller, Torsten; Heravi-Moussavi, Alireza; Cheng, Jeffrey B; Costello, Joseph F; Lorincz, Matthew C; Karimi, Mohammad M; Jones, Steven J M

2014-04-15

The assessment of expression and epigenomic status using sequencing based methods provides an unprecedented opportunity to identify and correlate allelic differences with epigenomic status. We present ALEA, a computational toolbox for allele-specific epigenomics analysis, which incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells. ALEA provides a customizable pipeline of command line tools for allele-specific analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers. The pipeline has been validated using human and hybrid mouse ChIP-seq and RNA-seq data. The package, test data and usage instructions are available online at http://www.bcgsc.ca/platform/bioinfo/software/alea CONTACT: : mkarimi1@interchange.ubc.ca or sjones@bcgsc.ca Supplementary information: Supplementary data are available at Bioinformatics online. © The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

MuffinInfo: HTML5-Based Statistics Extractor from Next-Generation Sequencing Data.

PubMed

Alic, Andy S; Blanquer, Ignacio

2016-09-01

Usually, the information known a priori about a newly sequenced organism is limited. Even resequencing the same organism can generate unpredictable output. We introduce MuffinInfo, a FastQ/Fasta/SAM information extractor implemented in HTML5 capable of offering insights into next-generation sequencing (NGS) data. Our new tool can run on any software or hardware environment, in command line or graphically, and in browser or standalone. It presents information such as average length, base distribution, quality scores distribution, k-mer histogram, and homopolymers analysis. MuffinInfo improves upon the existing extractors by adding the ability to save and then reload the results obtained after a run as a navigable file (also supporting saving pictures of the charts), by supporting custom statistics implemented by the user, and by offering user-adjustable parameters involved in the processing, all in one software. At the moment, the extractor works with all base space technologies such as Illumina, Roche, Ion Torrent, Pacific Biosciences, and Oxford Nanopore. Owing to HTML5, our software demonstrates the readiness of web technologies for mild intensive tasks encountered in bioinformatics.

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R.

PubMed

McCarthy, Davis J; Campbell, Kieran R; Lun, Aaron T L; Wills, Quin F

2017-04-15

Single-cell RNA sequencing (scRNA-seq) is increasingly used to study gene expression at the level of individual cells. However, preparing raw sequence data for further analysis is not a straightforward process. Biases, artifacts and other sources of unwanted variation are present in the data, requiring substantial time and effort to be spent on pre-processing, quality control (QC) and normalization. We have developed the R/Bioconductor package scater to facilitate rigorous pre-processing, quality control, normalization and visualization of scRNA-seq data. The package provides a convenient, flexible workflow to process raw sequencing reads into a high-quality expression dataset ready for downstream analysis. scater provides a rich suite of plotting tools for single-cell data and a flexible data structure that is compatible with existing tools and can be used as infrastructure for future software development. The open-source code, along with installation instructions, vignettes and case studies, is available through Bioconductor at http://bioconductor.org/packages/scater . davis@ebi.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

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

Marschman, Steven Craig

While low burn-up fuel [that characterized as having a burn-up of less than 45 gigawatt days per metric ton uranium (GWD/MTU)] has been stored for nearly three decades, the storage of high burn-up used fuels is more recent. The DOE has funded a High Burn-Up (HBU) Confirmatory Data Project to confirm the behavior of used high burn-up fuel under prototypic conditions. The Electric Power Research Institute (EPRI) is leading a project team to develop and implement the Test Plan to collect this data from a UNF dry storage system containing high burn-up fuel. As part of that project, 25 “sister”more » fuel rods have been selected, removed from assemblies, and placed in a fuel container ready for shipment to a national laboratory. This report documents that status of readiness to receive the fuel if that fuel were to be sent to Idaho National Laboratory (INL).« less

Amination of black liquor and the application in the ready-mixed wet mortar.

PubMed

Zheng, Dafeng; Zheng, Tao; Chen, Ran; Li, Xiaokang; Qiu, Xueqing

2018-01-01

In order to extend the application of black liquor (BL), amino group was introduced in lignin through Mannich reaction. The structure of the aminated black liquor (ABL) was characterized with FT-IR, elemental analysis, the zeta potential and the inherent viscosity. The foam generated by ABL was more stable, for the surface tension was lower. The results of the mortar test indicated that the water-retention rate of the fresh mortar incorporated with 0.3 wt% ABL was 89.1%; the consistency loss was about 39.7% after 4 h. When the dosage was less than 0.3 wt%, ABL could increase the bond strength of the hardened mortars. The results showed that ABL could be used as an effective ready-mixed wet mortar admixture. This study not only provided a new method to develop new mortar admixture, but also alleviated the pollution of BL.

Genetic characterization of K13965, a strain of Oak Vale virus from Western Australia.

PubMed

Quan, Phenix-Lan; Williams, David T; Johansen, Cheryl A; Jain, Komal; Petrosov, Alexandra; Diviney, Sinead M; Tashmukhamedova, Alla; Hutchison, Stephen K; Tesh, Robert B; Mackenzie, John S; Briese, Thomas; Lipkin, W Ian

2011-09-01

K13965, an uncharacterized virus, was isolated in 1993 from Anopheles annulipes mosquitoes collected in the Kimberley region of northern Western Australia. Here, we report its genomic sequence, identify it as a rhabdovirus, and characterize its phylogenetic relationships. The genome comprises a P' (C) and SH protein similar to the recently characterized Tupaia and Durham viruses, and shows overlap between G and L genes. Comparison of K13965 genome sequence to other rhabdoviruses identified K13965 as a strain of the unclassified Australian Oak Vale rhabdovirus, whose complete genome sequence we also determined. Phylogenetic analysis of N and L sequences indicated genetic relationship to a recently proposed Sandjima virus clade, although the Oak Vale virus sequences form a branch separate from the African members of that group. Copyright © 2011 Elsevier B.V. All rights reserved.

Differentiation of Trypanosoma cruzi I subgroups through characterization of cytochrome b gene sequences.

PubMed

Spotorno O, Angel E; Córdova, Luis; Solari I, Aldo

2008-12-01

To identify and characterize chilean samples of Trypanosoma cruzi and their association with hosts, the first 516 bp of the mitochondrial cytochrome b gene were sequenced from eight biological samples, and phylogenetically compared with other known 20 American sequences. The molecular characterization of these 28 sequences in a maximum likelihood phylogram (-lnL = 1255.12, tree length = 180, consistency index = 0.79) allowed the robust identification (bootstrap % > 99) of three previously known discrete typing units (DTU): DTU IIb, IIa, and I. An apparently undescribed new sequence found in four new chilean samples was detected and designated as DTU Ib; they were separated by 24.7 differences, but robustly related (bootstrap % = 97 in 500 replicates) to those of DTU I by sharing 12 substitutions, among which four were nonsynonymous ones. Such new DTU Ib was also robust (bootstrap % = 100), and characterized by 10 unambiguous substitutions, with a single nonsynonymous G to T change at site 409. The fact that two of such new sequences were found in parasites from a chilean endemic caviomorph rodent, Octodon degus, and that they were closely related to the ancient DTU I suggested old origins and a long association to caviomorph hosts.

The multilocus sequence typing network: mlst.net.

PubMed

Aanensen, David M; Spratt, Brian G

2005-07-01

The unambiguous characterization of strains of a pathogen is crucial for addressing questions relating to its epidemiology, population and evolutionary biology. Multilocus sequence typing (MLST), which defines strains from the sequences at seven house-keeping loci, has become the method of choice for molecular typing of many bacterial and fungal pathogens (and non-pathogens), and MLST schemes and strain databases are available for a growing number of prokaryotic and eukaryotic organisms. Sequence data are ideal for strain characterization as they are unambiguous, meaning strains can readily be compared between laboratories via the Internet. Laboratories undertaking MLST can quickly progress from sequencing the seven gene fragments to characterizing their strains and relating them to those submitted by others and to the population as a whole. We provide the gateway to a number of MLST schemes, each of which contain a set of tools for the initial characterization of strains, and methods for relating query strains to other strains of the species, including clustering based on differences in allelic profiles, phylogenetic trees based on concatenated sequences, and a recently developed method (eBURST) for identifying clonal complexes within a species and displaying the overall structure of the population. This network of MLST websites is available at http://www.mlst.net.

Metagenomic approaches for direct and cell culture evaluation of the virological quality of wastewater

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

Aw, Tiong Gim; Howe, Adina; Rose, Joan B.

2014-12-01

Genomic-based molecular techniques are emerging as powerful tools that allow a comprehensive characterization of water and wastewater microbiomes. Most recently, next generation sequencing (NGS) technologies which produce large amounts of sequence data are beginning to impact the field of environmental virology. In this study, NGS and bioinformatics have been employed for the direct detection and characterization of viruses in wastewater and of viruses isolated after cell culture. Viral particles were concentrated and purified from sewage samples by polyethylene glycol precipitation. Viral nucleic acid was extracted and randomly amplified prior to sequencing using Illumina technology, yielding a total of 18 millionmore » sequence reads. Most of the viral sequences detected could not be characterized, indicating the great viral diversity that is yet to be discovered. This sewage virome was dominated by bacteriophages and contained sequences related to known human pathogenic viruses such as adenoviruses (species B, C and F), polyomaviruses JC and BK and enteroviruses (type B). An array of other animal viruses was also found, suggesting unknown zoonotic viruses. This study demonstrated the feasibility of metagenomic approaches to characterize viruses in complex environmental water samples.« less

Secure Genomic Computation through Site-Wise Encryption

PubMed Central

Zhao, Yongan; Wang, XiaoFeng; Tang, Haixu

2015-01-01

Commercial clouds provide on-demand IT services for big-data analysis, which have become an attractive option for users who have no access to comparable infrastructure. However, utilizing these services for human genome analysis is highly risky, as human genomic data contains identifiable information of human individuals and their disease susceptibility. Therefore, currently, no computation on personal human genomic data is conducted on public clouds. To address this issue, here we present a site-wise encryption approach to encrypt whole human genome sequences, which can be subject to secure searching of genomic signatures on public clouds. We implemented this method within the Hadoop framework, and tested it on the case of searching disease markers retrieved from the ClinVar database against patients’ genomic sequences. The secure search runs only one order of magnitude slower than the simple search without encryption, indicating our method is ready to be used for secure genomic computation on public clouds. PMID:26306278

Customized workflow development and data modularization concepts for RNA-Sequencing and metatranscriptome experiments.

PubMed

Lott, Steffen C; Wolfien, Markus; Riege, Konstantin; Bagnacani, Andrea; Wolkenhauer, Olaf; Hoffmann, Steve; Hess, Wolfgang R

2017-11-10

RNA-Sequencing (RNA-Seq) has become a widely used approach to study quantitative and qualitative aspects of transcriptome data. The variety of RNA-Seq protocols, experimental study designs and the characteristic properties of the organisms under investigation greatly affect downstream and comparative analyses. In this review, we aim to explain the impact of structured pre-selection, classification and integration of best-performing tools within modularized data analysis workflows and ready-to-use computing infrastructures towards experimental data analyses. We highlight examples for workflows and use cases that are presented for pro-, eukaryotic and mixed dual RNA-Seq (meta-transcriptomics) experiments. In addition, we are summarizing the expertise of the laboratories participating in the project consortium "Structured Analysis and Integration of RNA-Seq experiments" (de.STAIR) and its integration with the Galaxy-workbench of the RNA Bioinformatics Center (RBC). Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Recovery of a Medieval Brucella melitensis Genome Using Shotgun Metagenomics

PubMed Central

Kay, Gemma L.; Sergeant, Martin J.; Giuffra, Valentina; Bandiera, Pasquale; Milanese, Marco; Bramanti, Barbara

2014-01-01

ABSTRACT Shotgun metagenomics provides a powerful assumption-free approach to the recovery of pathogen genomes from contemporary and historical material. We sequenced the metagenome of a calcified nodule from the skeleton of a 14th-century middle-aged male excavated from the medieval Sardinian settlement of Geridu. We obtained 6.5-fold coverage of a Brucella melitensis genome. Sequence reads from this genome showed signatures typical of ancient or aged DNA. Despite the relatively low coverage, we were able to use information from single-nucleotide polymorphisms to place the medieval pathogen genome within a clade of B. melitensis strains that included the well-studied Ether strain and two other recent Italian isolates. We confirmed this placement using information from deletions and IS711 insertions. We conclude that metagenomics stands ready to document past and present infections, shedding light on the emergence, evolution, and spread of microbial pathogens. PMID:25028426

Secure Genomic Computation through Site-Wise Encryption.

PubMed

Zhao, Yongan; Wang, XiaoFeng; Tang, Haixu

2015-01-01

Commercial clouds provide on-demand IT services for big-data analysis, which have become an attractive option for users who have no access to comparable infrastructure. However, utilizing these services for human genome analysis is highly risky, as human genomic data contains identifiable information of human individuals and their disease susceptibility. Therefore, currently, no computation on personal human genomic data is conducted on public clouds. To address this issue, here we present a site-wise encryption approach to encrypt whole human genome sequences, which can be subject to secure searching of genomic signatures on public clouds. We implemented this method within the Hadoop framework, and tested it on the case of searching disease markers retrieved from the ClinVar database against patients' genomic sequences. The secure search runs only one order of magnitude slower than the simple search without encryption, indicating our method is ready to be used for secure genomic computation on public clouds.

Career Readiness: Has Its Time Finally Come?

ERIC Educational Resources Information Center

DeWitt, Stephen

2012-01-01

In 2010, the Association for Career and Technical Education (ACTE) released a "What Is Career Ready?" definition. As the career-readiness definition explains, there is much overlap between "college readiness" and "career readiness," but academic preparedness for college alone is not enough to be truly career-ready.…

Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes

PubMed Central

2014-01-01

Background Although it is possible to recover the complete mitogenome directly from shotgun sequencing data, currently reported methods and pipelines are still relatively time consuming and costly. Using a sample of the Australian freshwater crayfish Engaeus lengana, we demonstrate that it is possible to achieve three-day turnaround time (four hours hands-on time) from tissue sample to NCBI-ready submission file through the integration of MiSeq sequencing platform, Nextera sample preparation protocol, MITObim assembly algorithm and MITOS annotation pipeline. Results The complete mitochondrial genome of the parastacid freshwater crayfish, Engaeus lengana, was recovered by modest shotgun sequencing (1.2 giga bases) using the Illumina MiSeq benchtop sequencing platform. Genome assembly using the MITObim mitogenome assembler recovered the mitochondrial genome as a single contig with a 97-fold mean coverage (min. = 17; max. = 138). The mitogenome consists of 15,934 base pairs and contains the typical 37 mitochondrial genes and a non-coding AT-rich region. The genome arrangement is similar to the only other published parastacid mitogenome from the Australian genus Cherax. Conclusions We infer that the gene order arrangement found in Cherax destructor is common to Australian crayfish and may be a derived feature of the southern hemisphere family Parastacidae. Further, we report to our knowledge, the simplest and fastest protocol for the recovery and assembly of complete mitochondrial genomes using the MiSeq benchtop sequencer. PMID:24484414

Preferential amino acid sequences in alumina-catalyzed peptide bond formation.

PubMed

Bujdák, J; Rode, B M

2002-05-21

The catalytic effect of activated alumina on amino acid condensation was investigated. The readiness of amino acids to form peptide sequences was estimated on the basis of the yield of dipeptides and was found to decrease in the order glycine (Gly), alanine (Ala), leucine (Leu), valine (Val), proline (Pro). For example, approximately 15% Gly was converted to the dipeptide (Gly(2)), 5% to cyclic anhydride (cyc(Gly(2))) and small amounts of tri- (Gly(3)) and tetrapeptide (Gly(4)) were formed after 28 days. On the other hand, only trace amounts of Pro(2) were formed from proline under the same conditions. Preferential formation of certain sequences was observed in the mixed reaction systems containing two amino acids. For example, almost ten times more Gly-Val than Val-Gly was formed in the Gly+Val reaction system. The preferred sequences can be explained on the basis of an inductive effect that side groups have on the nucleophilicity and electrophilicity, respectively, of the amino and carboxyl groups. A comparison with published data of amino acid reactions in other reaction systems revealed that the main trends of preferential sequence formation were the same as those described for the salt-induced peptide formation (SIPF) reaction. The results of this work and other previously published papers show that alumina and related mineral surfaces might have played a crucial role in the prebiotic formation of the first peptides on the primitive earth.

Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences.

PubMed

Zhang, Jianwei; Kudrna, Dave; Mu, Ting; Li, Weiming; Copetti, Dario; Yu, Yeisoo; Goicoechea, Jose Luis; Lei, Yang; Wing, Rod A

2016-10-15

Next generation sequencing technologies have revolutionized our ability to rapidly and affordably generate vast quantities of sequence data. Once generated, raw sequences are assembled into contigs or scaffolds. However, these assemblies are mostly fragmented and inaccurate at the whole genome scale, largely due to the inability to integrate additional informative datasets (e.g. physical, optical and genetic maps). To address this problem, we developed a semi-automated software tool-Genome Puzzle Master (GPM)-that enables the integration of additional genomic signposts to edit and build 'new-gen-assemblies' that result in high-quality 'annotation-ready' pseudomolecules. With GPM, loaded datasets can be connected to each other via their logical relationships which accomplishes tasks to 'group,' 'merge,' 'order and orient' sequences in a draft assembly. Manual editing can also be performed with a user-friendly graphical interface. Final pseudomolecules reflect a user's total data package and are available for long-term project management. GPM is a web-based pipeline and an important part of a Laboratory Information Management System (LIMS) which can be easily deployed on local servers for any genome research laboratory. The GPM (with LIMS) package is available at https://github.com/Jianwei-Zhang/LIMS CONTACTS: jzhang@mail.hzau.edu.cn or rwing@mail.arizona.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Is Your School Ready?

ERIC Educational Resources Information Center

Bracey, Gerald W.

2005-01-01

The Ready School, a concept endorsed by the National Education Goals Panel, focuses on getting schools ready for children to supplement the traditional approach of getting children ready for school. The author cites 10 qualities associated with Ready Schools and describes the eight-dimension Ready School Assessment project now being tested by the…

Changes in Helicopter Reliability/Maintainability Characteristics Over Time. Volume 2. Data Submitted by Helicopter Manufacturers

DTIC Science & Technology

1975-03-01

Quarterly Evaluation Report [ CH -54A] . . . S. TI. Eighth (8th) Quarterly CH -53 Readiness Report . . .. S-79 *.hrc.e parInation sequences are used In this...Total & Subsystem R Growth Parameters Table 2 CJF-46 Total Aircraft R~ Growth Statiatics Table 5 C7O-46 Subsystem R Growth Statistics Table 5 CH -46...UH-1 Navy. H-2 Navy, *-3 Navy# e OH-6 Army, H-19 Navy, H-19 Army, H-21 Air Force, H-21 Army. H-34 Army, H-34 Navy, H-37 Navy. H-37 Army, H-46 Navy, CH

Building block synthesis using the polymerase chain assembly method.

PubMed

Marchand, Julie A; Peccoud, Jean

2012-01-01

De novo gene synthesis allows the creation of custom DNA molecules without the typical constraints of traditional cloning assembly: scars, restriction site incompatibility, and the quest to find all the desired parts to name a few. Moreover, with the help of computer-assisted design, the perfect DNA molecule can be created along with its matching sequence ready to download. The challenge is to build the physical DNA molecules that have been designed with the software. Although there are several DNA assembly methods, this section presents and describes a method using the polymerase chain assembly (PCA).

Safe, Healthy and Ready to Succeed: Arizona School Readiness Key Performance Indicators

ERIC Educational Resources Information Center

Migliore, Donna E.

2006-01-01

"Safe, Healthy and Ready to Succeed: Arizona School Readiness Key Performance Indicators" presents a set of baseline measurements that gauge how well a statewide system of school readiness supports is addressing issues that affect Arizona children's readiness for school. The Key Performance Indicators (KPIs) measure the system, rather…

ESO Advanced Data Products for the Virtual Observatory

NASA Astrophysics Data System (ADS)

Retzlaff, J.; Delmotte, N.; Rite, C.; Rosati, P.; Slijkhuis, R.; Vandame, B.

2006-07-01

Advanced Data Products, that is, completely reduced, fully characterized science-ready data sets, play a crucial role for the success of the Virtual Observatory as a whole. We report on on-going work at ESO towards the creation and publication of Advanced Data Products in compliance with present VO standards on resource metadata. The new deep NIR multi-color mosaic of the GOODS/CDF-S region is used to showcase different aspects of the entire process: data reduction employing our MVM-based reduction pipeline, calibration and data characterization procedures, standardization of metadata content, and, finally, a prospect of the scientific potential illustrated by new results on deep galaxy number counts.

AVTA Federal Fleet PEV Readiness Data Logging and Characterization Study for NASA Glenn Research Center

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

Schey, Stephen; Francfort, Jim

The Advanced Vehicle Testing Activity’s study seeks to collect and evaluate data to validate the utilization of advanced plug-in electric vehicle (PEV) transportation. This report focuses on the NASA Glenn Research Center (GRC) fleet to identify daily operational characteristics of select vehicles and report findings on vehicle and mission characterizations to support the successful introduction of PEVs into the agencies’ fleets. Individual observations of these selected vehicles provide the basis for recommendations related to electric vehicle adoption and whether a battery electric vehicle or plug-in hybrid electric vehicle (collectively referred to as PEVs) can fulfill the mission requirements.

Characterization of DNA-protein interactions using high-throughput sequencing data from pulldown experiments

NASA Astrophysics Data System (ADS)

Moreland, Blythe; Oman, Kenji; Curfman, John; Yan, Pearlly; Bundschuh, Ralf

Methyl-binding domain (MBD) protein pulldown experiments have been a valuable tool in measuring the levels of methylated CpG dinucleotides. Due to the frequent use of this technique, high-throughput sequencing data sets are available that allow a detailed quantitative characterization of the underlying interaction between methylated DNA and MBD proteins. Analyzing such data sets, we first found that two such proteins cannot bind closer to each other than 2 bp, consistent with structural models of the DNA-protein interaction. Second, the large amount of sequencing data allowed us to find rather weak but nevertheless clearly statistically significant sequence preferences for several bases around the required CpG. These results demonstrate that pulldown sequencing is a high-precision tool in characterizing DNA-protein interactions. This material is based upon work supported by the National Science Foundation under Grant No. DMR-1410172.

Genotypes, antibiotic resistance, and virulence factors of staphylococci from ready-to-eat food.

PubMed

Podkowik, Magdalena; Bystroń, Jarosław; Bania, Jacek

2012-01-01

Sixty-seven staphylococcal isolates belonging to 12 species were obtained from 70 ready-to-eat food products. Staphylococcus aureus (n=25), and Staphylococcus epidermidis (n=13) were dominant. Susceptibility to penicillin, oxacillin, tetracycline, clindamycin, gentamicin, erythromycin, ciprofloxacin, and vancomycin was determined. All investigated S. aureus isolates were resistant to at least one antibiotic, and fifteen isolates were resistant to four and more antibiotics. Thirty-eight coagulase-negative staphylococci (CNS) isolates were resistant to at least one antibiotic, and seventeen to four and more antibiotics. Fifteen CNS isolates were mecA positive, and grew in the presence of 6 μg/mL oxacillin. All S. aureus isolates were mecA-negative. Arginine catabolic mobile element (ACME) was found in seven S. epidermidis isolates. Five S. epidermidis isolates harbored ica operon, ACME and were able to form biofilm. Three of them also possessed IS256 element and were mecA-positive. The expression of icaA gene was comparable in five ica-positive S. epidermidis isolates. One of six mecA positive S. epidermidis isolates was classified as sequence type (ST)155, one as ST110, and two as ST88. Two methicillin-resistant Staphylococcus epidermis (MRSE) belonged to new STs, that is, ST362, and ST363. Enterotoxin genes were found in 92% of S. aureus isolates. No enterotoxin gene was detected in analyzed CNS population. We show that ready-to-eat products are an important source of antibiotic-resistant CNS and potentially virulent strains of S. epidermidis, including genotypes undistinguishable from hospital-adapted clones.

A compiler and validator for flight operations on NASA space missions

NASA Astrophysics Data System (ADS)

Fonte, Sergio; Politi, Romolo; Capria, Maria Teresa; Giardino, Marco; De Sanctis, Maria Cristina

2016-07-01

In NASA missions the management and the programming of the flight systems is performed by a specific scripting language, the SASF (Spacecraft Activity Sequence File). In order to perform a check on the syntax and grammar it is necessary a compiler that stress the errors (eventually) found in the sequence file produced for an instrument on board the flight system. In our experience on Dawn mission, we developed VIRV (VIR Validator), a tool that performs checks on the syntax and grammar of SASF, runs a simulations of VIR acquisitions and eventually finds violation of the flight rules of the sequences produced. The project of a SASF compiler (SSC - Spacecraft Sequence Compiler) is ready to have a new implementation: the generalization for different NASA mission. In fact, VIRV is a compiler for a dialect of SASF; it includes VIR commands as part of SASF language. Our goal is to produce a general compiler for the SASF, in which every instrument has a library to be introduced into the compiler. The SSC can analyze a SASF, produce a log of events, perform a simulation of the instrument acquisition and check the flight rules for the instrument selected. The output of the program can be produced in GRASS GIS format and may help the operator to analyze the geometry of the acquisition.

Introducing the slime mold graph repository

NASA Astrophysics Data System (ADS)

Dirnberger, M.; Mehlhorn, K.; Mehlhorn, T.

2017-07-01

We introduce the slime mold graph repository or SMGR, a novel data collection promoting the visibility, accessibility and reuse of experimental data revolving around network-forming slime molds. By making data readily available to researchers across multiple disciplines, the SMGR promotes novel research as well as the reproduction of original results. While SMGR data may take various forms, we stress the importance of graph representations of slime mold networks due to their ease of handling and their large potential for reuse. Data added to the SMGR stands to gain impact beyond initial publications or even beyond its domain of origin. We initiate the SMGR with the comprehensive Kist Europe data set focusing on the slime mold Physarum polycephalum, which we obtained in the course of our original research. It contains sequences of images documenting growth and network formation of the organism under constant conditions. Suitable image sequences depicting the typical P. polycephalum network structures are used to compute sequences of graphs faithfully capturing them. Given such sequences, node identities are computed, tracking the development of nodes over time. Based on this information we demonstrate two out of many possible ways to begin exploring the data. The entire data set is well-documented, self-contained and ready for inspection at http://smgr.mpi-inf.mpg.de.

Assessing the School Readiness of Children in Jordan.

PubMed

Al-Hassan, Suha M; Lansford, Jennifer E

2009-01-01

In 2003, Jordan initiated a period of education reform, one component of which was an effort to improve readiness for first grade by opening public kindergartens. This study had three goals: (a) To describe the school readiness of Jordanian children; (b) To compare the first grade readiness of children who had and had not attended kindergarten; and (c) To compare the 2004 and 2007 readiness of children in areas that instituted kindergartens during that time period. Trained observers directly assessed 4,681 children's readiness, and teachers reported on children's social skills and behavioral readiness. At least 80% of children were rated as being almost or fully ready for first grade in each domain assessed. Children who had attended kindergarten were more ready for first grade than were children who had not attended kindergarten. In communities with newly established kindergartens, children were more ready for first grade in 2007 than in 2004.

Short Communication Phylogenetic Characterization of HIV Type 1 CRF01_AE V3 Envelope Sequences in Pregnant Women in Northern Vietnam

PubMed Central

Caridha, Rozina; Ha, Tran Thi Thanh; Gaseitsiwe, Simani; Hung, Pham Viet; Anh, Nguyen Mai; Bao, Nguyen Huy; Khang, Dinh Duy; Hien, Nguyen Tran; Cam, Phung Dac; Chiodi, Francesca

2012-01-01

Abstract Characterization of HIV-1 strains is important for surveillance of the HIV-1 epidemic. In Vietnam HIV-1-infected pregnant women often fail to receive the care they are entitled to. Here, we analyzed phylogenetically HIV-1 env sequences from 37 HIV-1-infected pregnant women from Ha Noi (n=22) and Hai Phong (n=15), where they delivered in 2005–2007. All carried CRF01_AE in the gp120 V3 region. In 21 women CRF01_AE was also found in the reverse transcriptase gene. We compared their env gp120 V3 sequences phylogenetically in a maximum likelihood tree to those of 198 other CRF01_AE sequences in Vietnam and 229 from neighboring countries, predominantly Thailand, from the HIV-1 database. Altogether 464 sequences were analyzed. All but one of the maternal sequences colocalized with sequences from northern Vietnam. The maternal sequences had evolved the least when compared to sequences collected in Ha Noi in 2002, as shown by analysis of synonymous and nonsynonymous changes, than to other Vietnamese sequences collected earlier and/or elsewhere. Since the HIV-1 epidemic in women in Vietnam may still be underestimated, characterization of HIV-1 in pregnant women is important to observe how HIV-1 has evolved and follow its molecular epidemiology. PMID:21936713

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

PubMed Central

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

2005-01-01

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

AVTA Federal Fleet PEV Readiness Data Logging and Characterization Study: Final Report

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

Schey, Stephen; Francfort, Jim

2015-06-01

Collect and evaluate data on federal fleet operations as part of the Advanced Vehicle Testing Activity’s Federal Fleet Vehicle Data Logging and Characterization Study. The Advanced Vehicle Testing Activity study seeks to collect and evaluate data to validate the utilization of advanced plug-in electric vehicle (PEV) transportation. This report summarizes the fleets studied to identify daily operational characteristics of select vehicles and report findings on vehicle and mission characterizations to support the successful introduction of PEVs into the agencies’ fleets. Individual observations of these selected vehicles provide the basis for recommendations related to electric vehicle adoption and whether a batterymore » electric vehicle or plug-in hybrid electric vehicle (collectively referred to as PEVs) can fulfill the mission requirements.« less

Getting Ready: The 2010-2011 Maryland School Readiness Report. Children Entering School Ready to Learn

ERIC Educational Resources Information Center

Maryland State Department of Education, 2011

2011-01-01

This report was developed in partnership with Ready At Five. It lays out the critical importance of children starting school fully prepared to succeed in kindergarten. Most importantly, the report shares what everyone has learned from the 2010-2011 Maryland Model for School Readiness (MMSR) data about the school readiness of Maryland's children:…

Could transformation mechanisms of acetylase-harboring pMdT1 plasmid be evaluated through proteomic tools in Escherichia coli?

PubMed

Magalhães, Pedro; Pinto, Luís; Gonçalves, Alexandre; Araújo, José Eduardo; Santos, Hugo M; Capelo, José Luis; Saénz, Yolanda; de Toro, María; Torres, Carmen; Chambon, Christophe; Hébraud, Michel; Poeta, Patrícia; Igrejas, Gilberto

2016-08-11

Escherichia coli is a commensal microorganism of the gastrointestinal tract of animals and humans and it is an excellent model organism for the study of antibiotic resistance mechanisms. The resistance transmission and other characteristics of bacteria are based on different types of gene transfer occurring throughout the bacterial evolution. One of which is horizontal gene transfer that allows us to understand the ability of bacteria to acquire new genes. One dimensional and two dimensional electrophoresis (2-DE) techniques were performed in order to identify and characterize the proteome of two E. coli strains: Electromax DH10B, a transformation-ready strain; and TF-Se20, the Electromax DH10B that contains the aac(6')-Ib-cr4-harboring pMdT1 plasmid. After 2-DE and subsequent analysis by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), it was possible to identify 76 distinct proteins on the TF-Se20 strain, whereas 71 had a known function. From Electromax DH10B strain, 72 different proteins were identified of which 71 were associated with a biological process. The protein of interest, aminoglycoside N-(6')-acetyltransferase type 1, was identified by MALDI-TOF MS. The liquid chromatography-tandem mass spectrometry (LC-MS/MS) technique was performed to determine its sequence. Seventy six percent of the acetylase sequence was reconstructed only in the TF-Se20 strain, representing the single protein associated to antibiotic resistance. MALDI-TOF MS and LC-MS/MS approaches allowed us to determine the total proteome of both strains, as well as the acetylase sequence. Both of them enhance the ability to obtain more accurate information about the mechanisms of antimicrobial resistance. The pMdT1 plasmid brings a new perspective in understanding the metabolic processes that lead to antibiotic resistance. This study highlights the importance of proteomics and bioinformatics in understanding mechanisms of gene transfer and antibiotic resistance. These two approaches allow to compare the protein expression in different samples, as well as different biological processes related to each protein. Copyright © 2016 Elsevier B.V. All rights reserved.

SACCHARIS: an automated pipeline to streamline discovery of carbohydrate active enzyme activities within polyspecific families and de novo sequence datasets.

PubMed

Jones, Darryl R; Thomas, Dallas; Alger, Nicholas; Ghavidel, Ata; Inglis, G Douglas; Abbott, D Wade

2018-01-01

Deposition of new genetic sequences in online databases is expanding at an unprecedented rate. As a result, sequence identification continues to outpace functional characterization of carbohydrate active enzymes (CAZymes). In this paradigm, the discovery of enzymes with novel functions is often hindered by high volumes of uncharacterized sequences particularly when the enzyme sequence belongs to a family that exhibits diverse functional specificities (i.e., polyspecificity). Therefore, to direct sequence-based discovery and characterization of new enzyme activities we have developed an automated in silico pipeline entitled: Sequence Analysis and Clustering of CarboHydrate Active enzymes for Rapid Informed prediction of Specificity (SACCHARIS). This pipeline streamlines the selection of uncharacterized sequences for discovery of new CAZyme or CBM specificity from families currently maintained on the CAZy website or within user-defined datasets. SACCHARIS was used to generate a phylogenetic tree of a GH43, a CAZyme family with defined subfamily designations. This analysis confirmed that large datasets can be organized into sequence clusters of manageable sizes that possess related functions. Seeding this tree with a GH43 sequence from Bacteroides dorei DSM 17855 (BdGH43b, revealed it partitioned as a single sequence within the tree. This pattern was consistent with it possessing a unique enzyme activity for GH43 as BdGH43b is the first described α-glucanase described for this family. The capacity of SACCHARIS to extract and cluster characterized carbohydrate binding module sequences was demonstrated using family 6 CBMs (i.e., CBM6s). This CBM family displays a polyspecific ligand binding profile and contains many structurally determined members. Using SACCHARIS to identify a cluster of divergent sequences, a CBM6 sequence from a unique clade was demonstrated to bind yeast mannan, which represents the first description of an α-mannan binding CBM. Additionally, we have performed a CAZome analysis of an in-house sequenced bacterial genome and a comparative analysis of B. thetaiotaomicron VPI-5482 and B. thetaiotaomicron 7330, to demonstrate that SACCHARIS can generate "CAZome fingerprints", which differentiate between the saccharolytic potential of two related strains in silico. Establishing sequence-function and sequence-structure relationships in polyspecific CAZyme families are promising approaches for streamlining enzyme discovery. SACCHARIS facilitates this process by embedding CAZyme and CBM family trees generated from biochemically to structurally characterized sequences, with protein sequences that have unknown functions. In addition, these trees can be integrated with user-defined datasets (e.g., genomics, metagenomics, and transcriptomics) to inform experimental characterization of new CAZymes or CBMs not currently curated, and for researchers to compare differential sequence patterns between entire CAZomes. In this light, SACCHARIS provides an in silico tool that can be tailored for enzyme bioprospecting in datasets of increasing complexity and for diverse applications in glycobiotechnology.

Reducing Operating Room Turnover Time for Robotic Surgery Using a Motor Racing Pit Stop Model.

PubMed

Souders, Colby P; Catchpole, Ken R; Wood, Lauren N; Solnik, Jonathon M; Avenido, Raymund M; Strauss, Paul L; Eilber, Karyn S; Anger, Jennifer T

2017-08-01

Operating room (OR) turnover time, time taken between one patient leaving the OR and the next entering, is an important determinant of OR utilization, a key value metric for hospital administrators. Surgical robots have increased the complexity and number of tasks required during an OR turnover, resulting in highly variable OR turnover times. We sought to streamline the turnover process and decrease robotic OR turnover times and increase efficiency. Direct observation of 45 pre-intervention robotic OR turnovers was performed. Following a previously successful model for handoffs, we employed concepts from motor racing pit stops, including briefings, leadership, role definition, task allocation and task sequencing. Turnover task cards for staff were developed, and card assignments were distributed for each turnover. Forty-one cases were observed post-intervention. Average total OR turnover time was 99.2 min (95% CI 88.0-110.3) pre-intervention and 53.2 min (95% CI 48.0-58.5) at 3 months post-intervention. Average room ready time from when the patient exited the OR until the surgical technician was ready to receive the next patient was 42.2 min (95% CI 36.7-47.7) before the intervention, which reduced to 27.2 min at 3 months (95% CI 24.7-29.7) post-intervention (p < 0.0001). Role definition, task allocation and sequencing, combined with a visual cue for ease-of-use, create efficient, and sustainable approaches to decreasing robotic OR turnover times. Broader system changes are needed to capitalize on that result. Pit stop and other high-risk industry models may inform approaches to the management of tasks and teams.

Maturity Assessment of Space Plug-and-Play Architecture

DTIC Science & Technology

2013-03-01

SSM SPA Service Module SRL System Readiness Level TAT Time-at-Tone TRA Technology Readiness Assessment TRL Technology Readiness Level USB Universal...maturity assessment—the Technology Readiness Level (TRL) process, the Integration Readiness Level (IRL) process, and the System Readiness Level ( SRL ...is an important hallmark of the SPA concept, and makes possible the composability and scalability of system designs that employ it. 14 4. SPA

Molecular characterization of Taenia multiceps isolates from Gansu Province, China by sequencing of mitochondrial cytochrome C oxidase subunit 1.

PubMed

Li, Wen Hui; Jia, Wan Zhong; Qu, Zi Gang; Xie, Zhi Zhou; Luo, Jian Xun; Yin, Hong; Sun, Xiao Lin; Blaga, Radu; Fu, Bao Quan

2013-04-01

A total of 16 Taenia multiceps isolates collected from naturally infected sheep or goats in Gansu Province, China were characterized by sequences of mitochondrial cytochrome c oxidase subunit 1 (cox1) gene. The complete cox1 gene was amplified for individual T. multiceps isolates by PCR, ligated to pMD18T vector, and sequenced. Sequence analysis indicated that out of 16 T. multiceps isolates 10 unique cox1 gene sequences of 1,623 bp were obtained with sequence variation of 0.12-0.68%. The results showed that the cox1 gene sequences were highly conserved among the examined T. multiceps isolates. However, they were quite different from those of the other Taenia species. Phylogenetic analysis based on complete cox1 gene sequences revealed that T. multiceps isolates were composed of 3 genotypes and distinguished from the other Taenia species.

Molecular Characterization of Taenia multiceps Isolates from Gansu Province, China by Sequencing of Mitochondrial Cytochrome C Oxidase Subunit 1

PubMed Central

Li, Wen Hui; Jia, Wan Zhong; Qu, Zi Gang; Xie, Zhi Zhou; Luo, Jian Xun; Yin, Hong; Sun, Xiao Lin; Blaga, Radu

2013-01-01

A total of 16 Taenia multiceps isolates collected from naturally infected sheep or goats in Gansu Province, China were characterized by sequences of mitochondrial cytochrome c oxidase subunit 1 (cox1) gene. The complete cox1 gene was amplified for individual T. multiceps isolates by PCR, ligated to pMD18T vector, and sequenced. Sequence analysis indicated that out of 16 T. multiceps isolates 10 unique cox1 gene sequences of 1,623 bp were obtained with sequence variation of 0.12-0.68%. The results showed that the cox1 gene sequences were highly conserved among the examined T. multiceps isolates. However, they were quite different from those of the other Taenia species. Phylogenetic analysis based on complete cox1 gene sequences revealed that T. multiceps isolates were composed of 3 genotypes and distinguished from the other Taenia species. PMID:23710087

A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies

PubMed Central

Cao, Yu; Fanning, Séamus; Proos, Sinéad; Jordan, Kieran; Srikumar, Shabarinath

2017-01-01

The development of next generation sequencing (NGS) techniques has enabled researchers to study and understand the world of microorganisms from broader and deeper perspectives. The contemporary advances in DNA sequencing technologies have not only enabled finer characterization of bacterial genomes but also provided deeper taxonomic identification of complex microbiomes which in its genomic essence is the combined genetic material of the microorganisms inhabiting an environment, whether the environment be a particular body econiche (e.g., human intestinal contents) or a food manufacturing facility econiche (e.g., floor drain). To date, 16S rDNA sequencing, metagenomics and metatranscriptomics are the three basic sequencing strategies used in the taxonomic identification and characterization of food-related microbiomes. These sequencing strategies have used different NGS platforms for DNA and RNA sequence identification. Traditionally, 16S rDNA sequencing has played a key role in understanding the taxonomic composition of a food-related microbiome. Recently, metagenomic approaches have resulted in improved understanding of a microbiome by providing a species-level/strain-level characterization. Further, metatranscriptomic approaches have contributed to the functional characterization of the complex interactions between different microbial communities within a single microbiome. Many studies have highlighted the use of NGS techniques in investigating the microbiome of fermented foods. However, the utilization of NGS techniques in studying the microbiome of non-fermented foods are limited. This review provides a brief overview of the advances in DNA sequencing chemistries as the technology progressed from first, next and third generations and highlights how NGS provided a deeper understanding of food-related microbiomes with special focus on non-fermented foods. PMID:29033905

Drop Tower Characterization of Army Research Lab (ARL)-Fabricated Thin-Film Lead Zirconate Titanate (PZT) Transducers

DTIC Science & Technology

2012-04-01

TRADE NAME, TRADEMARK, MANUFACTURER , OR OTHERWISE, DOES NOT CONSTITUTE OR IMPLY ITS ENDORSEMENT, RECOMMENDATION, OR FAVORING BY THE U.S. GOVERNMENT...TRADE NAMES USE OF TRADE NAMES OR MANUFACTURERS IN THIS REPORT DOES NOT CONSTITUTE AN OFFICIAL ENDORSEMENT OR APPROVAL OF THE USE OF...on Gel-Pak Ready for Noodle Wire Attachment ..................... 10 13. Waveshaper (on Right) Beside a 0.5-Inch Steel Ball

Family System of Advanced Charring Ablators for Planetary Exploration Missions

NASA Technical Reports Server (NTRS)

Congdon, William M.; Curry, Donald M.

2005-01-01

Advanced Ablators Program Objectives: 1) Flight-ready(TRL-6) ablative heat shields for deep-space missions; 2) Diversity of selection from family-system approach; 3) Minimum weight systems with high reliability; 4) Optimized formulations and processing; 5) Fully characterized properties; and 6) Low-cost manufacturing. Definition and integration of candidate lightweight structures. Test and analysis database to support flight-vehicle engineering. Results from production scale-up studies and production-cost analyses.

High Temperature Gas-Cooled Test Reactor Point Design: Summary Report

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

Sterbentz, James William; Bayless, Paul David; Nelson, Lee Orville

2016-01-01

A point design has been developed for a 200-MW high-temperature gas-cooled test reactor. The point design concept uses standard prismatic blocks and 15.5% enriched uranium oxycarbide fuel. Reactor physics and thermal-hydraulics simulations have been performed to characterize the capabilities of the design. In addition to the technical data, overviews are provided on the technology readiness level, licensing approach, and costs of the test reactor point design.

High Temperature Gas-Cooled Test Reactor Point Design: Summary Report

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

Sterbentz, James William; Bayless, Paul David; Nelson, Lee Orville

2016-03-01

A point design has been developed for a 200-MW high-temperature gas-cooled test reactor. The point design concept uses standard prismatic blocks and 15.5% enriched uranium oxycarbide fuel. Reactor physics and thermal-hydraulics simulations have been performed to characterize the capabilities of the design. In addition to the technical data, overviews are provided on the technology readiness level, licensing approach, and costs of the test reactor point design.

Robustness of Reconstructed Ancestral Protein Functions to Statistical Uncertainty.

PubMed

Eick, Geeta N; Bridgham, Jamie T; Anderson, Douglas P; Harms, Michael J; Thornton, Joseph W

2017-02-01

Hypotheses about the functions of ancient proteins and the effects of historical mutations on them are often tested using ancestral protein reconstruction (APR)-phylogenetic inference of ancestral sequences followed by synthesis and experimental characterization. Usually, some sequence sites are ambiguously reconstructed, with two or more statistically plausible states. The extent to which the inferred functions and mutational effects are robust to uncertainty about the ancestral sequence has not been studied systematically. To address this issue, we reconstructed ancestral proteins in three domain families that have different functions, architectures, and degrees of uncertainty; we then experimentally characterized the functional robustness of these proteins when uncertainty was incorporated using several approaches, including sampling amino acid states from the posterior distribution at each site and incorporating the alternative amino acid state at every ambiguous site in the sequence into a single "worst plausible case" protein. In every case, qualitative conclusions about the ancestral proteins' functions and the effects of key historical mutations were robust to sequence uncertainty, with similar functions observed even when scores of alternate amino acids were incorporated. There was some variation in quantitative descriptors of function among plausible sequences, suggesting that experimentally characterizing robustness is particularly important when quantitative estimates of ancient biochemical parameters are desired. The worst plausible case method appears to provide an efficient strategy for characterizing the functional robustness of ancestral proteins to large amounts of sequence uncertainty. Sampling from the posterior distribution sometimes produced artifactually nonfunctional proteins for sequences reconstructed with substantial ambiguity. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Sources of Foods That Are Ready-to-Consume ('Grazing Environments') Versus Requiring Additional Preparation ('Grocery Environments'): Implications for Food-Environment Research and Community Health.

PubMed

Lucan, Sean C; Maroko, Andrew R; Seitchik, Jason L; Yoon, Don; Sperry, Luisa E; Schechter, Clyde B

2018-03-14

Local businesses that offer foods may create different 'grazing environments' (characterized by sources of ready-to-consume foods) and 'grocery environments' (characterized by source of foods for later preparation). Such environments may be relevant to different populations at different times and may vary by neighborhood. In neighborhoods within two demographically distinct areas of the Bronx, NY [Area A (higher-poverty, greater minority representation, lesser vehicle ownership) vs. Area B], researchers assessed all storefront businesses for food offerings. Food offerings could be ready-to-consume or require additional preparation. 'Healthful' offerings included fruits and vegetables, whole grains, and nuts; 'less-healthful' offerings included 'refined sweets' and 'salty/fatty fare.' 'Food businesses' (those primarily focused on selling food) were distinguished from 'other businesses' (not focused primarily on food selling). Area A had a higher percentage of street segments on which foods were available (28.6% vs. 6.9% in Area B; difference 21.7% points [95% CI 17.0, 26.5]) and a higher percentage of businesses offering foods (46.9% vs. 41.7% in Area B; difference 5.2% points [95% CI - 2.0, 12.4]). 'Less-healthful' items predominated in both 'grazing environments' and overall environments ('grazing' plus 'grocery environments'; the environments researchers typically measure) in both Areas A and B. 'Other businesses' represented about 2/3 of all businesses and accounted for nearly 1/3 of all the businesses offering food in both geographic areas. The lower-income area with greater minority representation and less private transportation had more businesses offering foods on more streets. There was near-perfect overlap between 'grazing environments' and overall environments in both geographic areas. Future research should consider the extent of 'grazing' and 'grocery environments,' and when each might be most relevant to populations of interest.

Generation and Characterization of HIV-1 Transmitted and Founder Virus Consensus Sequence from Intravenous Drug Users in Xinjiang, China.

PubMed

Li, Fan; Ma, Liying; Feng, Yi; Hu, Jing; Ni, Na; Ruan, Yuhua; Shao, Yiming

2017-06-01

HIV-1 transmission in intravenous drug users (IDUs) has been characterized by high genetic multiplicity and suggests a greater challenge for HIV-1 infection blocking. We investigated a total of 749 sequences of full-length gp160 gene obtained by single genome sequencing (SGS) from 22 HIV-1 early infected IDUs in Xinjiang province, northwest China, and generated a transmitted and founder virus (T/F virus) consensus sequence (IDU.CON). The T/F virus was classified as subtype CRF07_BC and predicted to be CCR5-tropic virus. The variable region (V1, V2, and V4 loop) of IDU.CON showed length variation compared with the heterosexual T/F virus consensus sequence (HSX.CON) and homosexual T/F virus consensus sequence (MSM.CON). A total of 26 N-linked glycosylation sites were discovered in the IDU.CON sequence, which is less than that of MSM.CON and HSX.CON. Characterization of T/F virus from IDUs highlights the genetic make-up and complexity of virus near the moment of transmission or in early infection preceding systemic dissemination and is important toward the development of an effective HIV-1 preventive methods, including vaccines.

Medical Readiness of the Reserve Component.

PubMed

Brauner, Marygail K; Jackson, Timothy; Gayton, Elizabeth

2012-01-01

The reserve components (RCs) of the U.S. military must ensure that reservists are not only properly equipped and trained, but also medically ready to serve. Medical readiness means that service members are free from health-related conditions, including dental conditions, that could limit their ability to carry out their duties. Medically ready reservists require less medical and dental support in theater and fewer medical evacuations from theater, both of which save money and free assets for other purposes. This article identifies existing medical readiness requirements, quantifies the current status of RC medical readiness, identifies obstacles to achieving compliance, and suggests options for improving medical readiness in a cost-effective manner. The authors find that time and expense are the major barriers to the RCs achieving their overall goals for medical readiness. Recommendations include standardizing medical readiness criteria across services, improving data reporting and archiving processes, providing incentives to individuals and units to achieve medical readiness, and continuing to extend TRICARE coverage to reservists prior to deployment.

Simultaneous virus identification and characterization of severe unexplained pneumonia cases using a metagenomics sequencing technique.

PubMed

Zou, Xiaohui; Tang, Guangpeng; Zhao, Xiang; Huang, Yan; Chen, Tao; Lei, Mingyu; Chen, Wenbing; Yang, Lei; Zhu, Wenfei; Zhuang, Li; Yang, Jing; Feng, Zhaomin; Wang, Dayan; Wang, Dingming; Shu, Yuelong

2017-03-01

Many viruses can cause respiratory diseases in humans. Although great advances have been achieved in methods of diagnosis, it remains challenging to identify pathogens in unexplained pneumonia (UP) cases. In this study, we applied next-generation sequencing (NGS) technology and a metagenomic approach to detect and characterize respiratory viruses in UP cases from Guizhou Province, China. A total of 33 oropharyngeal swabs were obtained from hospitalized UP patients and subjected to NGS. An unbiased metagenomic analysis pipeline identified 13 virus species in 16 samples. Human rhinovirus C was the virus most frequently detected and was identified in seven samples. Human measles virus, adenovirus B 55 and coxsackievirus A10 were also identified. Metagenomic sequencing also provided virus genomic sequences, which enabled genotype characterization and phylogenetic analysis. For cases of multiple infection, metagenomic sequencing afforded information regarding the quantity of each virus in the sample, which could be used to evaluate each viruses' role in the disease. Our study highlights the potential of metagenomic sequencing for pathogen identification in UP cases.

MG-Digger: An Automated Pipeline to Search for Giant Virus-Related Sequences in Metagenomes

PubMed Central

Verneau, Jonathan; Levasseur, Anthony; Raoult, Didier; La Scola, Bernard; Colson, Philippe

2016-01-01

The number of metagenomic studies conducted each year is growing dramatically. Storage and analysis of such big data is difficult and time-consuming. Interestingly, analysis shows that environmental and human metagenomes include a significant amount of non-annotated sequences, representing a ‘dark matter.’ We established a bioinformatics pipeline that automatically detects metagenome reads matching query sequences from a given set and applied this tool to the detection of sequences matching large and giant DNA viral members of the proposed order Megavirales or virophages. A total of 1,045 environmental and human metagenomes (≈ 1 Terabase) were collected, processed, and stored on our bioinformatics server. In addition, nucleotide and protein sequences from 93 Megavirales representatives, including 19 giant viruses of amoeba, and 5 virophages, were collected. The pipeline was generated by scripts written in Python language and entitled MG-Digger. Metagenomes previously found to contain megavirus-like sequences were tested as controls. MG-Digger was able to annotate 100s of metagenome sequences as best matching those of giant viruses. These sequences were most often found to be similar to phycodnavirus or mimivirus sequences, but included reads related to recently available pandoraviruses, Pithovirus sibericum, and faustoviruses. Compared to other tools, MG-Digger combined stand-alone use on Linux or Windows operating systems through a user-friendly interface, implementation of ready-to-use customized metagenome databases and query sequence databases, adjustable parameters for BLAST searches, and creation of output files containing selected reads with best match identification. Compared to Metavir 2, a reference tool in viral metagenome analysis, MG-Digger detected 8% more true positive Megavirales-related reads in a control metagenome. The present work shows that massive, automated and recurrent analyses of metagenomes are effective in improving knowledge about the presence and prevalence of giant viruses in the environment and the human body. PMID:27065984

14 CFR 415.37 - Flight readiness and communications plan.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 14 Aeronautics and Space 4 2014-01-01 2014-01-01 false Flight readiness and communications plan... a Federal Launch Range § 415.37 Flight readiness and communications plan. (a) Flight readiness requirements. An applicant must designate an individual responsible for flight readiness. The applicant must...

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area.

PubMed

Nakano, Kazuma; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Minami, Maiko; Nakanishi, Tetsuhiro; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

2017-07-01

PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

Next-generation sequencing library preparation method for identification of RNA viruses on the Ion Torrent Sequencing Platform.

PubMed

Chen, Guiqian; Qiu, Yuan; Zhuang, Qingye; Wang, Suchun; Wang, Tong; Chen, Jiming; Wang, Kaicheng

2018-05-09

Next generation sequencing (NGS) is a powerful tool for the characterization, discovery, and molecular identification of RNA viruses. There were multiple NGS library preparation methods published for strand-specific RNA-seq, but some methods are not suitable for identifying and characterizing RNA viruses. In this study, we report a NGS library preparation method to identify RNA viruses using the Ion Torrent PGM platform. The NGS sequencing adapters were directly inserted into the sequencing library through reverse transcription and polymerase chain reaction, without fragmentation and ligation of nucleic acids. The results show that this method is simple to perform, able to identify multiple species of RNA viruses in clinical samples.

Measuring School Readiness: Conceptual and Practical Considerations

ERIC Educational Resources Information Center

Snow, Kyle L.

2006-01-01

Recent interest and investment in early childhood education as a means of promoting children's school readiness has prompted the need for clear definitions of school readiness. Traditionally school readiness has been viewed within a maturationist frame, based on a chronological set-point, which led to the emergence of readiness testing. Following…

Ready or Not: Recognizing and Preparing College-Ready Students

ERIC Educational Resources Information Center

Springer, Sheree E.; Wilson, Tonia J.; Dole, Janice A.

2015-01-01

Research shows that many students entering postsecondary education are unprepared for college reading demands. This article highlights college reading readiness according to four essential reading skills. We illustrate these skills by featuring vignettes of high school seniors who are college-ready and not college-ready. Then we contextualize the…

Characterization of circulating transfer RNA-Derived RNA fragments in cattle

USDA-ARS?s Scientific Manuscript database

The objective was to characterize naturally occurring circulating transfer RNA-derived RNA Fragments (tRFs) in cattle. Serum from eight clinically normal adult dairy cows was collected, and small non-coding RNAs were extracted immediately after collection and sequenced by Illumina MiSeq. Sequences a...

Nebula--a web-server for advanced ChIP-seq data analysis.

PubMed

Boeva, Valentina; Lermine, Alban; Barette, Camille; Guillouf, Christel; Barillot, Emmanuel

2012-10-01

ChIP-seq consists of chromatin immunoprecipitation and deep sequencing of the extracted DNA fragments. It is the technique of choice for accurate characterization of the binding sites of transcription factors and other DNA-associated proteins. We present a web service, Nebula, which allows inexperienced users to perform a complete bioinformatics analysis of ChIP-seq data. Nebula was designed for both bioinformaticians and biologists. It is based on the Galaxy open source framework. Galaxy already includes a large number of functionalities for mapping reads and peak calling. We added the following to Galaxy: (i) peak calling with FindPeaks and a module for immunoprecipitation quality control, (ii) de novo motif discovery with ChIPMunk, (iii) calculation of the density and the cumulative distribution of peak locations relative to gene transcription start sites, (iv) annotation of peaks with genomic features and (v) annotation of genes with peak information. Nebula generates the graphs and the enrichment statistics at each step of the process. During Steps 3-5, Nebula optionally repeats the analysis on a control dataset and compares these results with those from the main dataset. Nebula can also incorporate gene expression (or gene modulation) data during these steps. In summary, Nebula is an innovative web service that provides an advanced ChIP-seq analysis pipeline providing ready-to-publish results. Nebula is available at http://nebula.curie.fr/ Supplementary data are available at Bioinformatics online.

Acidovorax valerianellae sp. nov., a novel pathogen of lamb's lettuce [Valerianella locusta (L.) Laterr].

PubMed

Gardan, Louis; Stead, David E; Dauga, Catherine; Gillis, Moniek

2003-05-01

Bacterial spot disease of lamb's lettuce [Valerianella locusta (L.) Laterr.] was first observed in fields in 1991. This new bacterial disease is localized in western France in high-technology field production of lamb's lettuce for the preparation of ready-to-use salad. Nineteen strains isolated in 1992 and 1993 from typical black leaf spots of naturally infected lamb's lettuce were characterized and compared with reference strains of Acidovorax and Delftia. The pathogenicity of the 19 strains was confirmed by artificial inoculation. Biochemical and physiological tests, fatty acid profiles, DNA-DNA hybridization and other nucleic acid-based tests were performed. A numerical taxonomic analysis of the 19 lamb's lettuce strains showed a single homogeneous phenon closely related to previously described phytopathogenic taxa of the genus Acidovorax. DNA-DNA hybridization studies showed that the lamb's lettuce strains were 91-100% related to a representative strain, strain CFBP 4730(T), and constituted a discrete DNA hybridization group, indicating that they belong to the same novel species. Results from DNA-rRNA hybridization, 16S rRNA sequence analysis and fatty acid analysis studies confirmed that this novel species belongs to the beta-subclass of the Proteobacteria and, more specifically, to the family Comamonadaceae and the genus Acidovorax. The name Acidovorax valerianellae sp. nov. is proposed for this novel taxon of phytopathogenic bacteria. The type strain is strain CFBP 4730(T) (= NCPPB 4283(T)).

Isothermal circular-strand-displacement polymerization of DNA and microRNA in digital microfluidic devices.

PubMed

Giuffrida, Maria Chiara; Zanoli, Laura Maria; D'Agata, Roberta; Finotti, Alessia; Gambari, Roberto; Spoto, Giuseppe

2015-02-01

Nucleic-acid amplification is a crucial step in nucleic-acid-sequence-detection assays. The use of digital microfluidic devices to miniaturize amplification techniques reduces the required sample volume and the analysis time and offers new possibilities for process automation and integration in a single device. The recently introduced droplet polymerase-chain-reaction (PCR) amplification methods require repeated cycles of two or three temperature-dependent steps during the amplification of the nucleic-acid target sequence. In contrast, low-temperature isothermal-amplification methods have no need for thermal cycling, thus requiring simplified microfluidic-device features. Here, the combined use of digital microfluidics and molecular-beacon (MB)-assisted isothermal circular-strand-displacement polymerization (ICSDP) to detect microRNA-210 sequences is described. MicroRNA-210 has been described as the most consistently and predominantly upregulated hypoxia-inducible factor. The nmol L(-1)-pmol L(-1) detection capabilities of the method were first tested by targeting single-stranded DNA sequences from the genetically modified Roundup Ready soybean. The ability of the droplet-ICSDP method to discriminate between full-matched, single-mismatched, and unrelated sequences was also investigated. The detection of a range of nmol L(-1)-pmol L(-1) microRNA-210 solutions compartmentalized in nanoliter-sized droplets was performed, establishing the ability of the method to detect as little as 10(-18) mol of microRNA target sequences compartmentalized in 20 nL droplets. The suitability of the method for biological samples was tested by detecting microRNA-210 from transfected K562 cells.

Identification of short single disulfide-containing contryphans from the venom of cone snails using de novo mass spectrometry-based sequencing methods.

PubMed

Franklin, Jayaseelan Benjamin; Rajesh, Rajaian Pushpabai; Vinithkumar, Nambali Valsalan; Kirubagaran, Ramalingam

2017-06-15

We identified 12 short single disulfide-containing conopeptides from the venom of Conus coronatus, C. leopardus, C. lividus and C. zonatus. Interestingly, we detected the shortest contryphan sequence thus far characterized which contains only six amino acid residues. We also identified three distinct contryphan sequences of C. lividus without any proline residues and one sequence with an unusual post-translational modification (bromination of tryptophan). Furthermore, we characterized venom peptides of C. zonatus for the first time. Copyright © 2017 Elsevier Ltd. All rights reserved.

Generation of a total of 6483 expressed sequence tags from 60 day-old bovine whole fetus and fetal placenta.

PubMed

Oishi, M; Gohma, H; Lejukole, H Y; Taniguchi, Y; Yamada, T; Suzuki, K; Shinkai, H; Uenishi, H; Yasue, H; Sasaki, Y

2004-05-01

Expressed sequence tags (ESTs) generated based on characterization of clones isolated randomly from cDNA libraries are used to study gene expression profiles in specific tissues and to provide useful information for characterizing tissue physiology. In this study, two directionally cloned cDNA libraries were constructed from 60 day-old bovine whole fetus and fetal placenta. We have characterized 5357 and 1126 clones, and then identified 3464 and 795 unique sequences for the fetus and placenta cDNA libraries: 1851 and 504 showed homology to already identified genes, and 1613 and 291 showed no significant matches to any of the sequences in DNA databases, respectively. Further, we found 94 unique sequences overlapping in both the fetus and the placenta, leading to a catalog of 4165 genes expressed in 60 day-old fetus and placenta. The catalog is used to examine expression profile of genes in 60 day-old bovine fetus and placenta.

Blocks in cycles and k-commuting permutations.

PubMed

Moreno, Rutilo; Rivera, Luis Manuel

2016-01-01

We introduce and study k -commuting permutations. One of our main results is a characterization of permutations that k -commute with a given permutation. Using this characterization, we obtain formulas for the number of permutations that k -commute with a permutation [Formula: see text], for some cycle types of [Formula: see text]. Our enumerative results are related with integer sequences in "The On-line Encyclopedia of Integer Sequences", and in some cases provide new interpretations for such sequences.

Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias

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

Krishnakumar, Raga; Sinha, Anupama; Bird, Sara W.

Emerging sequencing technologies are allowing us to characterize environmental, clinical and laboratory samples with increasing speed and detail, including real-time analysis and interpretation of data. One example of this is being able to rapidly and accurately detect a wide range of pathogenic organisms, both in the clinic and the field. Genomes can have radically different GC content however, such that accurate sequence analysis can be challenging depending upon the technology used. Here, we have characterized the performance of the Oxford MinION nanopore sequencer for detection and evaluation of organisms with a range of genomic nucleotide bias. We have diagnosed themore » quality of base-calling across individual reads and discovered that the position within the read affects base-calling and quality scores. Finally, we have evaluated the performance of the current state-of-the-art neural network-based MinION basecaller, characterizing its behavior with respect to systemic errors as well as context- and sequence-specific errors. Overall, we present a detailed characterization the capabilities of the MinION in terms of generating high-accuracy sequence data from genomes with a wide range of nucleotide content. This study provides a framework for designing the appropriate experiments that are the likely to lead to accurate and rapid field-forward diagnostics.« less

Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias

DOE PAGES

Krishnakumar, Raga; Sinha, Anupama; Bird, Sara W.; ...

2018-02-16

Emerging sequencing technologies are allowing us to characterize environmental, clinical and laboratory samples with increasing speed and detail, including real-time analysis and interpretation of data. One example of this is being able to rapidly and accurately detect a wide range of pathogenic organisms, both in the clinic and the field. Genomes can have radically different GC content however, such that accurate sequence analysis can be challenging depending upon the technology used. Here, we have characterized the performance of the Oxford MinION nanopore sequencer for detection and evaluation of organisms with a range of genomic nucleotide bias. We have diagnosed themore » quality of base-calling across individual reads and discovered that the position within the read affects base-calling and quality scores. Finally, we have evaluated the performance of the current state-of-the-art neural network-based MinION basecaller, characterizing its behavior with respect to systemic errors as well as context- and sequence-specific errors. Overall, we present a detailed characterization the capabilities of the MinION in terms of generating high-accuracy sequence data from genomes with a wide range of nucleotide content. This study provides a framework for designing the appropriate experiments that are the likely to lead to accurate and rapid field-forward diagnostics.« less

Stop Trying to Make Kids "Ready" for Kindergarten

ERIC Educational Resources Information Center

Pretti-Frontczak, Kristie

2014-01-01

The author of this article asks: What is readiness for kindergarten? How do we know when a child is ready? Unfortunately, as with many topics in education reform and improvement, policy makers ignore the complex questions about readiness and instead focus narrowly on select variables. The focus for kindergarten readiness is on select literacy and…

The College Readiness Data Catalog Tool: User Guide. REL 2014-042

ERIC Educational Resources Information Center

Rodriguez, Sheila M.; Estacion, Angela

2014-01-01

As the name indicates, the College Readiness Data Catalog Tool focuses on identifying data that can indicate a student's college readiness. While college readiness indicators may also signal career readiness, many states, districts, and other entities, including the U.S. Virgin Islands (USVI), do not systematically collect career readiness…

E-Learning Readiness in Medicine: Turkish Family Medicine (FM) Physicians Case

ERIC Educational Resources Information Center

Parlakkiliç, Alaattin

2015-01-01

This research investigates e-learning readiness level of family medicine physicians (FM) in Turkey. The study measures the level of e-learning readiness of Turkish FM physicians by an online e-learning readiness survey. According to results five areas are ready at Turkish FM physicians but need a few improvements:…

Readiness Matters! The 2015-2016 Kindergarten Readiness Assessment Report

ERIC Educational Resources Information Center

Maryland State Department of Education, 2016

2016-01-01

As part of Maryland's ongoing commitment to early learning and school readiness, a comprehensive new Kindergarten Readiness Assessment (KRA) was administered for the second time. This assessment is part of the new Ready for Kindergarten: Maryland's Early Childhood Comprehensive Assessment System (R4K) that was developed to align to the state's…

Cloning, sequencing and characterization of lipase from a polyhydroxyalkanoate- (PHA-) synthesizing Pseudomonas resinovorans

USDA-ARS?s Scientific Manuscript database

Lipase gene (lip) of a biodegradable polyhydroxyalkanoate- (PHA-) synthesizing bacterium P. resinovorans NRRL B-2649 was cloned, sequenced and characterized by using consensus primers and PCR-based genome walking method. The ORF of the putative Lip (314 amino acids) and its active site (Ser111, Asp...

Effort versus reward: preparing samples for fungal community characterization in high-throughput sequencing surveys of soils

USDA-ARS?s Scientific Manuscript database

Next generation fungal amplicon sequencing is being used with increasing frequency to study fungal diversity in various ecosystems; however, the influence of sample preparation on the characterization of fungal community is poorly understood. We investigated the effects of four procedural modificati...

Molecular Characterization of an Avian Astrovirus

PubMed Central

Koci, Matthew D.; Seal, Bruce S.; Schultz-Cherry, Stacey

2000-01-01

Astroviruses are known to cause enteric disease in several animal species, including turkeys. However, only human astroviruses have been well characterized at the nucleotide level. Herein we report the nucleotide sequence, genomic organization, and predicted amino acid sequence of a turkey astrovirus isolated from poults with an emerging enteric disease. PMID:10846102

Automated synthesis of arabinoxylan-oligosaccharides enables characterization of antibodies that recognize plant cell wall glycans.

PubMed

Schmidt, Deborah; Schuhmacher, Frank; Geissner, Andreas; Seeberger, Peter H; Pfrengle, Fabian

2015-04-07

Monoclonal antibodies that recognize plant cell wall glycans are used for high-resolution imaging, providing important information about the structure and function of cell wall polysaccharides. To characterize the binding epitopes of these powerful molecular probes a library of eleven plant arabinoxylan oligosaccharides was produced by automated solid-phase synthesis. Modular assembly of oligoarabinoxylans from few building blocks was enabled by adding (2-naphthyl)methyl (Nap) to the toolbox of orthogonal protecting groups for solid-phase synthesis. Conjugation-ready oligosaccharides were obtained and the binding specificities of xylan-directed antibodies were determined on microarrays. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Efficient synthesis of dichlorodenafil, an unapproved sildenafil analogue appearing in non-prescription supplements.

PubMed

Kim, Jong Yup; Hwang, In Gyun; Oh, Jae Ho; Kang, Il Hyun; Kwon, Sung Won; Kim, Deukjoon

2013-01-01

We have developed an efficient synthesis of dichlorodenafil (4), an unapproved sildenafil analogue isolated from dietary supplements. Our sequence employs POCl(3)-mediated chlorination of readily available chloroacetyl compound 7 followed by selective hydrolysis of the chloro-heterocycle function. Our synthesis confirms the structure of the illegal additive, and will provide regulatory agencies with ready access to authentic standard samples of dichlorodenafil (4) to aid in their mission to protect the public from unapproved and potentially harmful erectile dysfunction (ED) drug analogues that are added to herbal and dietary supplements without providing users with appropriate toxicological or pharmacological information.

Unpacking the Black Box of the CSRP Intervention: The Mediating Roles of Teacher-child Relationship Quality and Self-regulation

PubMed Central

Jones, Stephanie M.; Bub, Kristen L.; Raver, C. Cybele

2014-01-01

This study examines the theory of change of the Chicago School Readiness Project (CSRP), testing a sequence of theory-derived mediating mechanisms including the quality of teacher-child relationships and children’s self-regulation. The CSRP is a multi-component teacher- and classroom-focused intervention, and its cluster-randomized efficacy trial was conducted in 35 Head Start-funded classrooms. A series of increasingly complex and conservative structural equation models indicate that the CSRP carries its effects on children’s academic and behavioral outcomes through changes in teacher-child relationship quality and children’s self-regulation. PMID:24729666

Fitchi: haplotype genealogy graphs based on the Fitch algorithm.

PubMed

Matschiner, Michael

2016-04-15

: In population genetics and phylogeography, haplotype genealogy graphs are important tools for the visualization of population structure based on sequence data. In this type of graph, node sizes are often drawn in proportion to haplotype frequencies and edge lengths represent the minimum number of mutations separating adjacent nodes. I here present Fitchi, a new program that produces publication-ready haplotype genealogy graphs based on the Fitch algorithm. http://www.evoinformatics.eu/fitchi.htm : michaelmatschiner@mac.com Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

[Modern methods application of genotyping of infectious diseases pathogens in the context of operational work of specialized anti-epidemic team during the XXII Olympic Winter Games and XI Paralympic Winter Games].

PubMed

Kuzkin, B P; Kulichenko, A N; Volynkina, A S; Efremenko, D V; Kuznetsova, I V; Kotenev, E S; Lyamkin, G I; Kartsev, N N; Klindukhov, V P

2015-01-01

This paper considers the experience of genotyping and sequencing technologies in laboratories of specialized anti-epidemic team (SAET) during the XXII Olympic Winter Games and XI Paralympic Winter Games of 2014 in Sochi. The work carried out during the pre-Olympic period on performance of readiness by SAET for these studies is analyzed. The results of genotyping strains of pathogens during the Olympic Games are presented. A conclusion about the effectiveness of the use of molecular genetic techniques in terms of SAET is made.

Automated Array Assembly, Phase 2

NASA Technical Reports Server (NTRS)

Daiello, R. V.

1978-01-01

The purpose of the overall program is to establish technological readiness and provide verification for the elements of a manufacturing sequence which would ultimately be suitable for the large-scale production of silicon solar-array modules at a selling price of less than $500/kW. A program and process plan for accomplishing this objective was developed and put into operation. Three junction-formation processes are shown; since cost analysis shows that they do not differ greatly in cost, each should be considered for technical merits and possible future cost reduction. The progress made in the various process steps of the plan is described, and conclusions are presented.

E-health readiness assessment framework in iran.

PubMed

Rezai-Rad, M; Vaezi, R; Nattagh, F

2012-01-01

Concept of e-readiness is used in many areas such as e-business, e-commerce, e-government, and e-banking. In terms of healthcare, e-readiness is a rather new concept, and is propounded under the title of E-healthcare. E-health readiness refers to the readiness of communities and healthcare institutions for the expected changes brought by programs related to Information and Communications Technology (lCT). The present research is conducted aiming at designing E-health Readiness Assessment Framework (EHRAF) in Iran. The e-health readiness assessment framework was designed based on reviewing literature on e-readiness assessment models and opinions of ICT and health experts. In the next step, Delphi method was used to develop and test the designed framework. Three questionnaires developed to test and modify the model while determining weights of the indices; afterward they were either sent to experts through email or delivered to them in face. The designed framework approved with 4 dimensions, 11 constituents and 58 indices. Technical readiness had the highest importance coefficient (0.256099), and the other dimensions were of the next levels of coefficient importance: core readiness (0.25520), social communication readiness (0.244658), and engagement readiness (0.244039). The framework presents the movement route and investment priorities in e-health in Iran. The proposed framework is a good instrument for measuring the e-readiness in health centers in Iran, and for identifying strengths and weaknesses of these centers to access ICT and its implementation for more effectiveness and for analyzing digital divide between them, as well.

E-Health Readiness Assessment Framework in Iran

PubMed Central

Rezai-Rad, M; Vaezi, R; Nattagh, F

2012-01-01

Background: Concept of e-readiness is used in many areas such as e-business, e-commerce, e-government, and e-banking. In terms of healthcare, e-readiness is a rather new concept, and is propounded under the title of E-healthcare. E-health readiness refers to the readiness of communities and healthcare institutions for the expected changes brought by programs related to Information and Communications Technology (lCT). The present research is conducted aiming at designing E-health Readiness Assessment Framework (EHRAF) in Iran. Methods: The e-health readiness assessment framework was designed based on reviewing literature on e-readiness assessment models and opinions of ICT and health experts. In the next step, Delphi method was used to develop and test the designed framework. Three questionnaires developed to test and modify the model while determining weights of the indices; afterward they were either sent to experts through email or delivered to them in face. Results: The designed framework approved with 4 dimensions, 11 constituents and 58 indices. Technical readiness had the highest importance coefficient (0.256099), and the other dimensions were of the next levels of coefficient importance: core readiness (0.25520), social communication readiness (0.244658), and engagement readiness (0.244039). Conclusion: The framework presents the movement route and investment priorities in e-health in Iran. The proposed framework is a good instrument for measuring the e-readiness in health centers in Iran, and for identifying strengths and weaknesses of these centers to access ICT and its implementation for more effectiveness and for analyzing digital divide between them, as well. PMID:23304661

Fast Dissemination of New HIV-1 CRF02/A1 Recombinants in Pakistan

PubMed Central

Chen, Yue; Hora, Bhavna; DeMarco, Todd; Shah, Sharaf Ali; Ahmed, Manzoor; Sanchez, Ana M.; Su, Chang; Carter, Meredith; Stone, Mars; Hasan, Rumina; Hasan, Zahra; Busch, Michael P.; Denny, Thomas N.; Gao, Feng

2016-01-01

A number of HIV-1 subtypes are identified in Pakistan by characterization of partial viral gene sequences. Little is known whether new recombinants are generated and how they disseminate since whole genome sequences for these viruses have not been characterized. Near full-length genome (NFLG) sequences were obtained by amplifying two overlapping half genomes or next generation sequencing from 34 HIV-1-infected individuals in Pakistan. Phylogenetic tree analysis showed that the newly characterized sequences were 16 subtype As, one subtype C, and 17 A/G recombinants. Further analysis showed that all 16 subtype A1 sequences (47%), together with the vast majority of sequences from Pakistan from other studies, formed a tight subcluster (A1a) within the subtype A1 clade, suggesting that they were derived from a single introduction. More in-depth analysis of 17 A/G NFLG sequences showed that five shared similar recombination breakpoints as in CRF02 (15%) but were phylogenetically distinct from the prototype CRF02 by forming a tight subcluster (CRF02a) while 12 (38%) were new recombinants between CRF02a and A1a or a divergent A1b viruses. Unique recombination patterns among the majority of the newly characterized recombinants indicated ongoing recombination. Interestingly, recombination breakpoints in these CRF02/A1 recombinants were similar to those in prototype CRF02 viruses, indicating that recombination at these sites more likely generate variable recombinant viruses. The dominance and fast dissemination of new CRF02a/A1 recombinants over prototype CRF02 suggest that these recombinant have more adapted and may become major epidemic strains in Pakistan. PMID:27973597

Characterization of alanine to valine sequence variants in the Fc region of nivolumab biosimilar produced in Chinese hamster ovary cells.

PubMed

Li, Yantao; Fu, Tuo; Liu, Tao; Guo, Huaizu; Guo, Qingcheng; Xu, Jin; Zhang, Dapeng; Qian, Weizhu; Dai, Jianxin; Li, Bohua; Guo, Yajun; Hou, Sheng; Wang, Hao

2016-07-01

Nivolumab is a therapeutic fully human IgG4 antibody to programmed death 1 (PD-1). In this study, a nivolumab biosimilar, which was produced in our laboratory, was analyzed and characterized. Sequence variants that contain undesired amino acid sequences may cause concern during biosimilar bioprocess development. We found that low levels of sequence variants were detected in the heavy chain of the nivolumab biosimilar by ultra performance liquid chromatography (UPLC) and tandem mass spectrometry. It was further identified with UPLC-MS/MS by IdeS or trypsin digestion. The sequence variant was confirmed through addition of synthetic mutant peptide. Subsequently, the mixing base signal of normal and mutant sequence was detected through DNA sequencing. The relative levels of mutant A424V in the Fc region of the heavy chain have been detected and demonstrated to be 12.25% and 13.54%, via base peak intensity (BPI) and UV chromatography of the tryptic peptide mapping, respectively. A424V variant was also quantified by real-time PCR (RT-PCR) at the DNA and RNA level, which was 19.2% and 16.8%, respectively. The relative content of the mutant was consistent at the DNA, RNA and protein level, indicating that the A424V mutation may have little influence at transcriptional or translational levels. These results demonstrate that orthogonal state-of-the-art techniques such as LC- UV- MS and RT-PCR should be implemented to characterize recombinant proteins and cell lines for development of biosimilars. Our study suggests that it is important to establish an integrated and effective analytical method to monitor and characterize sequence variants during antibody drug development, especially for antibody biosimilar products.

Evidence based practice readiness: A concept analysis.

PubMed

Schaefer, Jessica D; Welton, John M

2018-01-15

To analyse and define the concept "evidence based practice readiness" in nurses. Evidence based practice readiness is a term commonly used in health literature, but without a clear understanding of what readiness means. Concept analysis is needed to define the meaning of evidence based practice readiness. A concept analysis was conducted using Walker and Avant's method to clarify the defining attributes of evidence based practice readiness as well as antecedents and consequences. A Boolean search of PubMed and Cumulative Index for Nursing and Allied Health Literature was conducted and limited to those published after the year 2000. Eleven articles met the inclusion criteria for this analysis. Evidence based practice readiness incorporates personal and organisational readiness. Antecedents include the ability to recognize the need for evidence based practice, ability to access and interpret evidence based practice, and a supportive environment. The concept analysis demonstrates the complexity of the concept and its implications for nursing practice. The four pillars of evidence based practice readiness: nursing, training, equipping and leadership support are necessary to achieve evidence based practice readiness. Nurse managers are in the position to address all elements of evidence based practice readiness. Creating an environment that fosters evidence based practice can improve patient outcomes, decreased health care cost, increase nurses' job satisfaction and decrease nursing turnover. © 2018 John Wiley & Sons Ltd.

Organizational Readiness for Change and Opinions toward Treatment Innovations

PubMed Central

Fuller, Bret E.; Rieckmann, Traci; Nunes, Edward V.; Miller, Michael; Arfken, Cynthia; Edmundson, Eldon; McCarty, Dennis

2007-01-01

Program administrators and staff in treatment programs participating in the National Drug Abuse Treatment Clinical Trials Network (CTN) completed surveys to characterize participating programs and practitioners. A two-level random effects regression model assessed the influence of Organizational Readiness for Change (ORC) and organizational attributes on opinions toward the use of four evidence-based practices (manualized treatments, medication, integrated mental health services, and motivational incentives) and practices with less empirical support (confrontation and noncompliance discharge). The ORC Scales suggested greater support for evidence-based practices in programs where staff perceived more program need for improvement, better Internet access, higher levels of peer influence, more opportunities for professional growth, a stronger sense of organizational mission and more organizational stress. Support for confrontation and noncompliance discharge, in contrast, was strong when staff saw less opportunity for professional growth, weaker peer influence, less Internet access, and perceived less organizational stress. The analysis provides evidence of the ORC’s utility in assessing agency strengths and needs during the implementation of evidence-based practices. PMID:17434708

Program Setup Time and Learning Curves associated with "ready to fly" Drone Mapping Hardware and Software.

NASA Astrophysics Data System (ADS)

Wilcox, T.

2016-12-01

How quickly can students (and educators) get started using a "ready to fly" UAS and popular publicly available photogrammetric mapping software for student research at the undergraduate level? This poster presentation focuses on the challenges of starting up your own drone-mapping program for undergraduate research in a compressed timescale of three months. Particular focus will be given to learning the operation of the platforms, hardware and software interface challenges, and using these electronic systems in real-world field settings that pose a range of physical challenges to both operators and equipment. We will be using a combination of the popular DJI Phantom UAS and Pix4D mapping software to investigate mass wasting processes and potential hazards present in public lands popular with recreational users. Projects are aimed at characterizing active geological hazards that operate on short timescales and may include gully headwall erosion in Flaming Geyser State Park and potential landslide instability within Capital State Forest, both in the Puget Sound region of Washington State.

Identification, quantitation, and method validation for flavan-3-ols in fermented ready-to-drink teas from the Italian market using HPLC-UV/DAD and LC-MS/MS.

PubMed

Cordero, Chiara; Canale, Francesca; Del Rio, Daniele; Bicchi, Carlo

2009-11-01

The present study is focused on flavan-3-ols characterizing the antioxidant properties of fermented tea (Camellia sinensis). These bioactive compounds, object of nutritional claims in commercial products, should be quantified with rigorous analytical procedures whose accuracy and precision have been stated with a certain level of confidence. An HPLC-UV/DAD method, able to detect and quantify flavan-3-ols in infusions and ready-to-drink teas, has been developed for routine analysis and validated by characterizing several performance parameters. The accuracy assessment has been run through a series of LC-MS/MS analyses. Epigallocatechin, (+)-catechin, (-)-epigallocatechingallate, (-)-epicatechin, (-)-gallocatechingallate, (-)-epicatechingallate, and (-)-catechingallate were chosen as markers of the polyphenolic fraction. Quantitative results showed that samples obtained from tea leaves infusion were richer in polyphenolic antioxidants than those obtained through other industrial processes. The influence of shelf-life and packaging material on the flavan-3-ols content was also considered; markers decreased, with an exponential trend, as a function of time within the shelf life while packaging materials demonstrated to influence differently the flavan-3-ol fraction composition over time. The method presented here provides quantitative results with a certain level of confidence and is suitable for a routine quality control of iced teas whose antioxidant properties are object of nutritional claim.

The Factor Structure of the CIBS-II-Readiness Assessment

ERIC Educational Resources Information Center

Gotch, Chad M.; French, Brian F.

2011-01-01

The Brigance Comprehensive Inventory of Basic Skills-II (CIBS-II)-Readiness form is a diagnostic battery intended for children aged 5 and 6 years. The CIBS-II-Readiness is a new version of the CIBS-Revised-Readiness and includes updated normative information on a larger representative sample in comparison to the CIBS-Revised-Readiness. Empirical…

Ready or Not...? Teen Sexuality and the Troubling Discourse of Readiness

ERIC Educational Resources Information Center

Ashcraft, Catherine

2006-01-01

In this article, I explore how talk about being "ready" or "not ready" for sex shapes teen and adult understandings of sexuality. I argue that this "discourse of readiness" poses serious threats to teens' identity development, sexual decision making, and educators efforts to help them through these processes. To illustrate, I draw from my…

Assessment of the Florida College and Career Readiness Initiative: Year 2 Report

ERIC Educational Resources Information Center

Mokher, Christine; Jacobson, Lou

2014-01-01

The Florida College and Career Readiness Initiative is a statewide policy that mandates college placement testing of 11th-graders who meet high school graduation criteria but are unlikely to meet college readiness criteria. Students who score below college-ready on the Postsecondary Education Readiness Test (PERT) are required to take math and…

Children Entering School Ready to Learn: 2010-2011 Maryland Model for School Readiness

ERIC Educational Resources Information Center

Maryland State Department of Education, 2009

2009-01-01

The report shares what everyone has learned from the 2010-2011 Maryland Model for School Readiness (MMSR) data about the school readiness of Maryland's children: statewide, by subgroups, and for each of Maryland's 24 local jurisdictions. Some of the highlights are: (1) The percentage of Maryland kindergarteners fully ready to start school…

M-Readiness Assessment Model Development and Validation: Investigation of Readiness Index and Factors Affecting Readiness

ERIC Educational Resources Information Center

Bakhsh, Muhammad; Mahmood, Amjad; Sangi, Nazir Ahmed

2018-01-01

It is important for distance learning institutions to be well prepared before designing and implementing any new technology based learning system to justify the investment and minimize failure risk. It can be achieved by systematically assessing the readiness of all stakeholders. This paper first proposes an m-readiness assessment process and…

Evaluation of anonymous and expressed sequence tag derived polymorphic microsatellite markers in the tobacco budworm Heliothis virescens (Lepidoptera: noctuidae)

USDA-ARS?s Scientific Manuscript database

Polymorphic genetic markers were identified and characterized using a partial genomic library of Heliothis virescens enriched for simple sequence repeats (SSR) and nucleotide sequences of expressed sequence tags (EST). Nucleotide sequences of 192 clones from the partial genomic library yielded 147 u...

A signal-amplified electrochemical DNA biosensor incorporated with a colorimetric internal control for Vibrio cholerae detection using shelf-ready reagents.

PubMed

Low, Kim-Fatt; Zain, Zainiharyati Mohd; Yean, Chan Yean

2017-01-15

A novel enzyme/nanoparticle-based DNA biosensing platform with dual colorimetric/electrochemical approach has been developed for the sequence-specific detection of the bacterium Vibrio cholerae, the causative agent of acute diarrheal disease in cholera. This assay platform exploits the use of shelf-stable and ready-to-use (shelf-ready) reagents to greatly simplify the bioanalysis procedures, allowing the assay platform to be more amenable to point-of-care applications. To assure maximum diagnosis reliability, an internal control (IC) capable of providing instant validation of results was incorporated into the assay. The microbial target, single-stranded DNA amplified with asymmetric PCR, was quantitatively detected via electrochemical stripping analysis of gold nanoparticle-loaded latex microspheres as a signal-amplified hybridization tag, while the incorporated IC was analyzed using a simplified horseradish peroxidase enzyme-based colorimetric scheme by simple visual observation of enzymatic color development. The platform showed excellent diagnostic sensitivity and specificity (100%) when challenged with 145 clinical isolate-spiked fecal specimens. The limits of detection were 0.5ng/ml of genomic DNA and 10 colony-forming units (CFU)/ml of bacterial cells with dynamic ranges of 0-100ng/ml (R 2 =0.992) and log 10 (1-10 4 CFU/ml) (R 2 =0.9918), respectively. An accelerated stability test revealed that the assay reagents were stable at temperatures of 4-37°C, with an estimated ambient shelf life of 200 days. The versatility of the biosensing platform makes it easily adaptable for quantitative detection of other microbial pathogens. Copyright © 2016 Elsevier B.V. All rights reserved.

Understanding Treatment Readiness in Recently Assessed, Pre-Treatment Substance Abusers

PubMed Central

Rapp, Richard C.; Xu, Jiangmin; Carr, Carey A.; Timothy Lane, D.; Redko, Cristina; Wang, Jichuan; Carlson, Robert G.

2007-01-01

The goal of this study was to more fully understand readiness for treatment in a pre-treatment sample of 446 substance abusers. Structural Equation Modeling (SEM) was used to: (1) examine the relationships between readiness factors identified in the Pre-Treatment Readiness Scale; and (2) identify the effects of predisposing, illness, and inhibiting determinants on the factors. As with in-treatment samples, Problem Recognition was found to influence Treatment Readiness, although through a different intervening factor, Desire for Change rather than Desire for Help. A fourth factor, Treatment Reluctance, was also influenced by the Desire for Change factor. Fixed characteristics such as age and gender had minimal influences on readiness factors, as did inhibiting characteristics that reflected recent functioning. Illness characteristics including drug severity and perceived treatment barriers had a more robust influence on readiness factors. This study provides an increased understanding of readiness for treatment among pre-treatment substance abusers and also supported the construct validity of the Pre-Treatment Readiness Scale. PMID:19274847

Detection of microRNAs in color space.

PubMed

Marco, Antonio; Griffiths-Jones, Sam

2012-02-01

Deep sequencing provides inexpensive opportunities to characterize the transcriptional diversity of known genomes. The AB SOLiD technology generates millions of short sequencing reads in color-space; that is, the raw data is a sequence of colors, where each color represents 2 nt and each nucleotide is represented by two consecutive colors. This strategy is purported to have several advantages, including increased ability to distinguish sequencing errors from polymorphisms. Several programs have been developed to map short reads to genomes in color space. However, a number of previously unexplored technical issues arise when using SOLiD technology to characterize microRNAs. Here we explore these technical difficulties. First, since the sequenced reads are longer than the biological sequences, every read is expected to contain linker fragments. The color-calling error rate increases toward the 3(') end of the read such that recognizing the linker sequence for removal becomes problematic. Second, mapping in color space may lead to the loss of the first nucleotide of each read. We propose a sequential trimming and mapping approach to map small RNAs. Using our strategy, we reanalyze three published insect small RNA deep sequencing datasets and characterize 22 new microRNAs. A bash shell script to perform the sequential trimming and mapping procedure, called SeqTrimMap, is available at: http://www.mirbase.org/tools/seqtrimmap/ antonio.marco@manchester.ac.uk Supplementary data are available at Bioinformatics online.

T-R Cycle Characterization and Imaging: Advanced Diagnostic Methodology for Petroleum Reservoir and Trap Detection and Delineation

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

Ernest A. Mancini

Characterization of stratigraphic sequences (T-R cycles or sequences) included outcrop studies, well log analysis and seismic reflection interpretation. These studies were performed by researchers at the University of Alabama, Wichita State University and McGill University. The outcrop, well log and seismic characterization studies were used to develop a depositional sequence model, a T-R cycle (sequence) model, and a sequence stratigraphy predictive model. The sequence stratigraphy predictive model developed in this study is based primarily on the modified T-R cycle (sequence) model. The T-R cycle (sequence) model using transgressive and regressive systems tracts and aggrading, backstepping, and infilling intervals or sectionsmore » was found to be the most appropriate sequence stratigraphy model for the strata in the onshore interior salt basins of the Gulf of Mexico to improve petroleum stratigraphic trap and specific reservoir facies imaging, detection and delineation. The known petroleum reservoirs of the Mississippi Interior and North Louisiana Salt Basins were classified using T-R cycle (sequence) terminology. The transgressive backstepping reservoirs have been the most productive of oil, and the transgressive backstepping and regressive infilling reservoirs have been the most productive of gas. Exploration strategies were formulated using the sequence stratigraphy predictive model and the classification of the known petroleum reservoirs utilizing T-R cycle (sequence) terminology. The well log signatures and seismic reflector patterns were determined to be distinctive for the aggrading, backstepping and infilling sections of the T-R cycle (sequence) and as such, well log and seismic data are useful for recognizing and defining potential reservoir facies. The use of the sequence stratigraphy predictive model, in combination with the knowledge of how the distinctive characteristics of the T-R system tracts and their subdivisions are expressed in well log patterns and seismic reflection configurations and terminations, improves the ability to identify and define the limits of potential stratigraphic traps and the stratigraphic component of combination stratigraphic and structural traps and the associated continental, coastal plain and marine potential reservoir facies. The assessment of the underdeveloped and undiscovered reservoirs and resources in the Mississippi Interior and North Louisiana Salt Basins resulted in the confirmation of the Monroe Uplift as a feature characterized by a major regional unconformity, which serves as a combination stratigraphic and structural trap with a significant stratigraphic component, and the characterization of a developing play in southwest Alabama, which involves a stratigraphic trap, located updip near the pinchout of the potential reservoir facies. Potential undiscovered and underdeveloped reservoirs in the onshore interior salt basins are identified as Jurassic and Cretaceous aggrading continental and coastal, backstepping nearshore marine and marine shelf, and infilling fluvial, deltaic, coastal plain and marine shelf.« less

Screening, Isolation and Identification of Probiotic Producing Lactobacillus acidophilus Strains EMBS081 & EMBS082 by 16S rRNA Gene Sequencing.

PubMed

Chandok, Harshpreet; Shah, Pratik; Akare, Uday Raj; Hindala, Maliram; Bhadoriya, Sneha Singh; Ravi, G V; Sharma, Varsha; Bandaru, Srinivas; Rathore, Pragya; Nayarisseri, Anuraj

2015-09-01

16S rDNA sequencing which has gained wide popularity amongst microbiologists for the molecular characterization and identification of newly discovered isolates provides accurate identification of isolates down to the level of sub-species (strain). Its most important advantage over the traditional biochemical characterization methods is that it can provide an accurate identification of strains with atypical phenotypic characters as well. The following work is an application of 16S rRNA gene sequencing approach to identify a novel species of Probiotic Lactobacillus acidophilus. The sample was collected from pond water samples of rural and urban areas of Krishna district, Vijayawada, Andhra Pradesh, India. Subsequently, the sample was serially diluted and the aliquots were incubated for a suitable time period following which the suspected colony was subjected to 16S rDNA sequencing. The sequence aligned against other species was concluded to be a novel, Probiotic L. acidophilus bacteria, further which were named L. acidophilus strain EMBS081 & EMBS082. After the sequence characterization, the isolate was deposited in GenBank Database, maintained by the National Centre for Biotechnology Information NCBI. The sequence can also be retrieve from EMBL and DDBJ repositories with accession numbers JX255677 and KC150145.

Characterization of a new apple luteovirus identified by high-throughput sequencing.

PubMed

Liu, Huawei; Wu, Liping; Nikolaeva, Ekaterina; Peter, Kari; Liu, Zongrang; Mollov, Dimitre; Cao, Mengji; Li, Ruhui

2018-05-15

'Rapid Apple Decline' (RAD) is a newly emerging problem of young, dwarf apple trees in the Northeastern USA. The affected trees show trunk necrosis, cracking and canker before collapse in summer. In this study, we discovered and characterized a new luteovirus from apple trees in RAD-affected orchards using high-throughput sequencing (HTS) technology and subsequent Sanger sequencing. Illumina NextSeq sequencing was applied to total RNAs prepared from three diseased apple trees. Sequence reads were de novo assembled, and contigs were annotated by BLASTx. RT-PCR and 5'/3' RACE sequencing were used to obtain the complete genome of a new virus. RT-PCR was used to detect the virus. Three common apple viruses and a new luteovirus were identified from the diseased trees by HTS and RT-PCR. Sequence analyses of the complete genome of the new virus show that it is a new species of the genus Luteovirus in the family Luteoviridae. The virus is graft transmissible and detected by RT-PCR in apple trees in a couple of orchards. A new luteovirus and/or three known viruses were found to be associated with RAD. Molecular characterization of the new luteovirus provides important information for further investigation of its distribution and etiological role.

From genomics to functional markers in the era of next-generation sequencing.

PubMed

Salgotra, R K; Gupta, B B; Stewart, C N

2014-03-01

The availability of complete genome sequences, along with other genomic resources for Arabidopsis, rice, pigeon pea, soybean and other crops, has revolutionized our understanding of the genetic make-up of plants. Next-generation DNA sequencing (NGS) has facilitated single nucleotide polymorphism discovery in plants. Functionally-characterized sequences can be identified and functional markers (FMs) for important traits can be developed at an ever-increasing ease. FMs are derived from sequence polymorphisms found in allelic variants of a functional gene. Linkage disequilibrium-based association mapping and homologous recombinants have been developed for identification of "perfect" markers for their use in crop improvement practices. Compared with many other molecular markers, FMs derived from the functionally characterized sequence genes using NGS techniques and their use provide opportunities to develop high-yielding plant genotypes resistant to various stresses at a fast pace.

Team-based learning in therapeutics workshop sessions.

PubMed

Beatty, Stuart J; Kelley, Katherine A; Metzger, Anne H; Bellebaum, Katherine L; McAuley, James W

2009-10-01

To implement team-based learning in the workshop portion of a pathophysiology and therapeutics sequence of courses to promote integration of concepts across the pharmacy curriculum, provide a consistent problem-solving approach to patient care, and determine the impact on student perceptions of professionalism and teamwork. Team-based learning was incorporated into the workshop portion of 3 of 6 pathophysiology and therapeutics courses. Assignments that promoted team-building and application of key concepts were created. Readiness assurance tests were used to assess individual and team understanding of course materials. Students consistently scored 20% higher on team assessments compared with individual assessments. Mean professionalism and teamwork scores were significantly higher after implementation of team-based learning; however, this improvement was not considered educationally significant. Approximately 91% of students felt team-based learning improved understanding of course materials and 93% of students felt teamwork should continue in workshops. Team-based learning is an effective teaching method to ensure a consistent approach to problem-solving and curriculum integration in workshop sessions for a pathophysiology and therapeutics course sequence.

Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons

PubMed Central

Krishnaswami, Suguna Rani; Grindberg, Rashel V; Novotny, Mark; Venepally, Pratap; Lacar, Benjamin; Bhutani, Kunal; Linker, Sara B; Pham, Son; Erwin, Jennifer A; Miller, Jeremy A; Hodge, Rebecca; McCarthy, James K; Kelder, Martin; McCorrison, Jamison; Aevermann, Brian D; Fuertes, Francisco Diez; Scheuermann, Richard H; Lee, Jun; Lein, Ed S; Schork, Nicholas; McConnell, Michael J; Gage, Fred H; Lasken, Roger S

2016-01-01

A protocol is described for sequencing the transcriptome of a cell nucleus. Nuclei are isolated from specimens and sorted by FACS, cDNA libraries are constructed and RNA-seq is performed, followed by data analysis. Some steps follow published methods (Smart-seq2 for cDNA synthesis and Nextera XT barcoded library preparation) and are not described in detail here. Previous single-cell approaches for RNA-seq from tissues include cell dissociation using protease treatment at 30 °C, which is known to alter the transcriptome. We isolate nuclei at 4 °C from tissue homogenates, which cause minimal damage. Nuclear transcriptomes can be obtained from postmortem human brain tissue stored at −80 °C, making brain archives accessible for RNA-seq from individual neurons. The method also allows investigation of biological features unique to nuclei, such as enrichment of certain transcripts and precursors of some noncoding RNAs. By following this procedure, it takes about 4 d to construct cDNA libraries that are ready for sequencing. PMID:26890679

PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens.

PubMed

Spahn, Philipp N; Bath, Tyler; Weiss, Ryan J; Kim, Jihoon; Esko, Jeffrey D; Lewis, Nathan E; Harismendy, Olivier

2017-11-20

Large-scale genetic screens using CRISPR/Cas9 technology have emerged as a major tool for functional genomics. With its increased popularity, experimental biologists frequently acquire large sequencing datasets for which they often do not have an easy analysis option. While a few bioinformatic tools have been developed for this purpose, their utility is still hindered either due to limited functionality or the requirement of bioinformatic expertise. To make sequencing data analysis of CRISPR/Cas9 screens more accessible to a wide range of scientists, we developed a Platform-independent Analysis of Pooled Screens using Python (PinAPL-Py), which is operated as an intuitive web-service. PinAPL-Py implements state-of-the-art tools and statistical models, assembled in a comprehensive workflow covering sequence quality control, automated sgRNA sequence extraction, alignment, sgRNA enrichment/depletion analysis and gene ranking. The workflow is set up to use a variety of popular sgRNA libraries as well as custom libraries that can be easily uploaded. Various analysis options are offered, suitable to analyze a large variety of CRISPR/Cas9 screening experiments. Analysis output includes ranked lists of sgRNAs and genes, and publication-ready plots. PinAPL-Py helps to advance genome-wide screening efforts by combining comprehensive functionality with user-friendly implementation. PinAPL-Py is freely accessible at http://pinapl-py.ucsd.edu with instructions and test datasets.

Simultaneous identification and molecular characterization of viruses associated with an apple tree with mosaic symptom

USDA-ARS?s Scientific Manuscript database

We conducted genomic sequencing to identify viruses associated with mosaic disease of an apple tree using the high-throughput sequencing (HTS) Illumina RNA-seq platform. The objective was to examine if rapid identification and characterization of viruses could be effectively achieved by RNA-seq anal...

Genotype-by-sequencing of the plant-pathogenic fungi Pyrenophora teres and Sphaerulina musiva utilizing Ion Torrent sequence technology

USDA-ARS?s Scientific Manuscript database

The characterization of genes determining compatibility or incompatibility between plant pathogenic fungi and their hosts is important for the management of crop disease. The major focus of these interactions has typically been the identification and characterization of host genes, but it is equally...

Isolation and characterization of microsatellite markers in Fraser fir (Abies fraseri)

Treesearch

S.A. Josserand; K.M. Potter; G. Johnson; J.A. Bowen; J. Frampton; C.D. Nelson

2006-01-01

We describe the isolation and characterization of 14 microsatellite loci from Fraser fir (Abies fraseri). These markers originated from cloned inserts enriched for DNA sequences containing tandem di- and tri-nucleotide repeats. In total, 36 clones were selected, sequenced and evaluated. Polymerase chain reaction (PCR) primers for 14 of these...

Molecular characterization and phylogenetic analysis of Citrus viroid VI variants from citrus in China

USDA-ARS?s Scientific Manuscript database

Citrus viroid VI (CVd-VI) was originally found from citrus and persimmon in Japan. We report here the identification and molecular characterization of CVd-VI from four production regions of China. A total of 90 cDNA clones from nine infected citrus cultivars were sequenced. The sequence homologies o...

Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping

USDA-ARS?s Scientific Manuscript database

The application of genotyping by sequencing (GBS) approaches, combined with data imputation methodologies, is narrowing the genetic knowledge gap between major and understudied, minor crops. GBS is an excellent tool to characterize the genomic structure of recently domesticated (~200 years) and unde...

Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum.

PubMed

Isakov, Ofer; Bordería, Antonio V; Golan, David; Hamenahem, Amir; Celniker, Gershon; Yoffe, Liron; Blanc, Hervé; Vignuzzi, Marco; Shomron, Noam

2015-07-01

The study of RNA virus populations is a challenging task. Each population of RNA virus is composed of a collection of different, yet related genomes often referred to as mutant spectra or quasispecies. Virologists using deep sequencing technologies face major obstacles when studying virus population dynamics, both experimentally and in natural settings due to the relatively high error rates of these technologies and the lack of high performance pipelines. In order to overcome these hurdles we developed a computational pipeline, termed ViVan (Viral Variance Analysis). ViVan is a complete pipeline facilitating the identification, characterization and comparison of sequence variance in deep sequenced virus populations. Applying ViVan on deep sequenced data obtained from samples that were previously characterized by more classical approaches, we uncovered novel and potentially crucial aspects of virus populations. With our experimental work, we illustrate how ViVan can be used for studies ranging from the more practical, detection of resistant mutations and effects of antiviral treatments, to the more theoretical temporal characterization of the population in evolutionary studies. Freely available on the web at http://www.vivanbioinfo.org : nshomron@post.tau.ac.il Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

The concept of readiness to change.

PubMed

Dalton, Cindy C; Gottlieb, Laurie N

2003-04-01

Readiness is associated with change, yet there is little understanding of this construct. The purpose of this study was to examine readiness; its referents, associated factors and the resulting consequences. In the course of nursing five clients living with multiple sclerosis over a 7-month period using a Reflective Practice Model, data were systematically gathered using open-ended and then more focused questioning. Data collected during 42 client encounters (28 face-to-face encounters; 14 telephone contacts) were analysed using Chinn and Kramer's concept analysis technique. Findings. The concept of readiness was inductively derived. Readiness is both a state and a process. Before clients can create change they need to become ready to change. A number of factors trigger readiness. These include when: (a) clients perceive that a health concern is not going to resolve, (b) a change in a client's physical condition takes on new significance, (c) clients feel better able to manage their stress, (d) clients have sufficient energy, (e) clients perceive that they have adequate support in undertaking change. When one or more of these factors is present clients become ready to consider change. The process of readiness involves recognizing the need to change, weighing the costs and benefits and, when benefits outweigh costs, planning for change. The desire to change and to take action determines clients' degree of readiness. When they experience a high degree of readiness they report less anger, less depression, and view their condition in a more positive light. In contrast, when they experience a low degree of readiness they report feeling depressed, afraid and vulnerable in the face of change. Nursing has an important role to play in creating conditions to support change. To fulfil this role, nurses need to be able to assess readiness for change and the factors that enable it and then to intervene in ways that facilitate readiness.

Molecular characterization of a novel Nucleorhabdovirus from black currant identified by high-throughput sequencing

USDA-ARS?s Scientific Manuscript database

Contigs with sequence similarities to several nucleorhabdoviruses were identified by high-throughput sequencing analysis from a black currant (Ribes nigrum L.) cultivar. The complete genomic sequence of this new nucleorhabdovirus is 14,432 nucleotides. Its genomic organization is typical of nucleorh...

Use of Sequence-Independent, Single-Primer-Amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses

USDA-ARS?s Scientific Manuscript database

Current technologies with next generation sequencing have revolutionized metagenomics analysis of clinical samples. To achieve the non-selective amplification and recovery of low abundance genetic sequences, a simplified Sequence-Independent, Single-Primer Amplification (SISPA) technique in combinat...

Characterization of Hepatitis C Virus (HCV) Envelope Diversification from Acute to Chronic Infection within a Sexually Transmitted HCV Cluster by Using Single-Molecule, Real-Time Sequencing

PubMed Central

Ho, Cynthia K. Y.; Raghwani, Jayna; Koekkoek, Sylvie; Liang, Richard H.; Van der Meer, Jan T. M.; Van Der Valk, Marc; De Jong, Menno; Pybus, Oliver G.

2016-01-01

ABSTRACT In contrast to other available next-generation sequencing platforms, PacBio single-molecule, real-time (SMRT) sequencing has the advantage of generating long reads albeit with a relatively higher error rate in unprocessed data. Using this platform, we longitudinally sampled and sequenced the hepatitis C virus (HCV) envelope genome region (1,680 nucleotides [nt]) from individuals belonging to a cluster of sexually transmitted cases. All five subjects were coinfected with HIV-1 and a closely related strain of HCV genotype 4d. In total, 50 samples were analyzed by using SMRT sequencing. By using 7 passes of circular consensus sequencing, the error rate was reduced to 0.37%, and the median number of sequences was 612 per sample. A further reduction of insertions was achieved by alignment against a sample-specific reference sequence. However, in vitro recombination during PCR amplification could not be excluded. Phylogenetic analysis supported close relationships among HCV sequences from the four male subjects and subsequent transmission from one subject to his female partner. Transmission was characterized by a strong genetic bottleneck. Viral genetic diversity was low during acute infection and increased upon progression to chronicity but subsequently fluctuated during chronic infection, caused by the alternate detection of distinct coexisting lineages. SMRT sequencing combines long reads with sufficient depth for many phylogenetic analyses and can therefore provide insights into within-host HCV evolutionary dynamics without the need for haplotype reconstruction using statistical algorithms. IMPORTANCE Next-generation sequencing has revolutionized the study of genetically variable RNA virus populations, but for phylogenetic and evolutionary analyses, longer sequences than those generated by most available platforms, while minimizing the intrinsic error rate, are desired. Here, we demonstrate for the first time that PacBio SMRT sequencing technology can be used to generate full-length HCV envelope sequences at the single-molecule level, providing a data set with large sequencing depth for the characterization of intrahost viral dynamics. The selection of consensus reads derived from at least 7 full circular consensus sequencing rounds significantly reduced the intrinsic high error rate of this method. We used this method to genetically characterize a unique transmission cluster of sexually transmitted HCV infections, providing insight into the distinct evolutionary pathways in each patient over time and identifying the transmission-associated genetic bottleneck as well as fluctuations in viral genetic diversity over time, accompanied by dynamic shifts in viral subpopulations. PMID:28077634

SNP Discovery by Illumina-Based Transcriptome Sequencing of the Olive and the Genetic Characterization of Turkish Olive Genotypes Revealed by AFLP, SSR and SNP Markers

PubMed Central

Kaya, Hilal Betul; Cetin, Oznur; Kaya, Hulya; Sahin, Mustafa; Sefer, Filiz; Kahraman, Abdullah; Tanyolac, Bahattin

2013-01-01

Background The olive tree (Olea europaea L.) is a diploid (2n = 2x = 46) outcrossing species mainly grown in the Mediterranean area, where it is the most important oil-producing crop. Because of its economic, cultural and ecological importance, various DNA markers have been used in the olive to characterize and elucidate homonyms, synonyms and unknown accessions. However, a comprehensive characterization and a full sequence of its transcriptome are unavailable, leading to the importance of an efficient large-scale single nucleotide polymorphism (SNP) discovery in olive. The objectives of this study were (1) to discover olive SNPs using next-generation sequencing and to identify SNP primers for cultivar identification and (2) to characterize 96 olive genotypes originating from different regions of Turkey. Methodology/Principal Findings Next-generation sequencing technology was used with five distinct olive genotypes and generated cDNA, producing 126,542,413 reads using an Illumina Genome Analyzer IIx. Following quality and size trimming, the high-quality reads were assembled into 22,052 contigs with an average length of 1,321 bases and 45 singletons. The SNPs were filtered and 2,987 high-quality putative SNP primers were identified. The assembled sequences and singletons were subjected to BLAST similarity searches and annotated with a Gene Ontology identifier. To identify the 96 olive genotypes, these SNP primers were applied to the genotypes in combination with amplified fragment length polymorphism (AFLP) and simple sequence repeats (SSR) markers. Conclusions/Significance This study marks the highest number of SNP markers discovered to date from olive genotypes using transcriptome sequencing. The developed SNP markers will provide a useful source for molecular genetic studies, such as genetic diversity and characterization, high density quantitative trait locus (QTL) analysis, association mapping and map-based gene cloning in the olive. High levels of genetic variation among Turkish olive genotypes revealed by SNPs, AFLPs and SSRs allowed us to characterize the Turkish olive genotype. PMID:24058483

Comparison Studies of Reading Readiness Skills Acquisition by Different Methods: Formal Reading Readiness Program, Informal Reading Readiness Program, and a Kindergarten Science Program.

ERIC Educational Resources Information Center

Quorn, Kerry Charles; Yore, Larry Dean

1978-01-01

Evaluates the effectiveness of two dissimilar programs, SAPA and the First Talking Alphabet (FTA), upon the acquisition of reading readiness skills of kindergarten pupils. Compares the effects of four different programs (SAPA, FTA, an informal language development program, and a control) on the reading readiness of kindergarten pupils. (GA)

Readiness to change as a moderator of outcome in transdiagnostic treatment

PubMed Central

BOSWELL, JAMES F.; SAUER, SHANNON E.; GALLAGHER, MATTHEW W.; DELGADO, NICOLE; BARLOW, DAVID H.

2012-01-01

Initial symptom severity is a client characteristic associated with psychotherapy outcome, although this relationship is not well-understood. Readiness to change is a factor that may influence this relationship. This study tested readiness as a moderator of the relationship between initial severity and symptom change. Data were derived from an RCT examining the efficacy of a transdiagnostic CBT treatment. Readiness was assessed with the URICA, and symptom and functioning outcomes were assessed. Multiple regression models indicated that severity was associated with less overall change, yet readiness moderated this relationship. At higher levels of readiness, the effect of initial severity on outcome was essentially reversed; for clients with higher initial readiness, higher levels of severity were associated with greater change. PMID:22607634

Molecular characterization of a novel Luteovirus from peach identified by high-throughput sequencing

USDA-ARS?s Scientific Manuscript database

Contigs with sequence homologies to Cherry-associated luteovirus were identified by high-throughput sequencing analysis of two peach accessions undergoing quarantine testing. The complete genomic sequences of the two isolates of this virus are 5,819 and 5,814 nucleotides. Their genome organization i...

Long-read sequencing and de novo assembly of a Chinese genome

USDA-ARS?s Scientific Manuscript database

Short-read sequencing has enabled the de novo assembly of several individual human genomes, but with inherent limitations in characterizing repeat elements. Here we sequence a Chinese individual HX1 by single-molecule real-time (SMRT) long-read sequencing, construct a physical map by NanoChannel arr...

Accurate phylogenetic classification of DNA fragments based onsequence composition

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

McHardy, Alice C.; Garcia Martin, Hector; Tsirigos, Aristotelis

2006-05-01

Metagenome studies have retrieved vast amounts of sequenceout of a variety of environments, leading to novel discoveries and greatinsights into the uncultured microbial world. Except for very simplecommunities, diversity makes sequence assembly and analysis a verychallenging problem. To understand the structure a 5 nd function ofmicrobial communities, a taxonomic characterization of the obtainedsequence fragments is highly desirable, yet currently limited mostly tothose sequences that contain phylogenetic marker genes. We show that forclades at the rank of domain down to genus, sequence composition allowsthe very accurate phylogenetic 10 characterization of genomic sequence.We developed a composition-based classifier, PhyloPythia, for de novophylogenetic sequencemore » characterization and have trained it on adata setof 340 genomes. By extensive evaluation experiments we show that themethodis accurate across all taxonomic ranks considered, even forsequences that originate fromnovel organisms and are as short as 1kb.Application to two metagenome datasets 15 obtained from samples ofphosphorus-removing sludge showed that the method allows the accurateclassification at genus level of most sequence fragments from thedominant populations, while at the same time correctly characterizingeven larger parts of the samples at higher taxonomic levels.« less

Biochemical, transcriptomic and proteomic analyses of digestion in the scorpion Tityus serrulatus: insights into function and evolution of digestion in an ancient arthropod.

PubMed

Fuzita, Felipe J; Pinkse, Martijn W H; Patane, José S L; Juliano, Maria A; Verhaert, Peter D E M; Lopes, Adriana R

2015-01-01

Scorpions are among the oldest terrestrial arthropods and they have passed through small morphological changes during their evolutionary history on land. They are efficient predators capable of capturing and consuming large preys and due to envenomation these animals can become a human health challenge. Understanding the physiology of scorpions can not only lead to evolutionary insights but also is a crucial step in the development of control strategies. However, the digestive process in scorpions has been scarcely studied. In this work, we describe the combinatory use of next generation sequencing, proteomic analysis and biochemical assays in order to investigate the digestive process in the yellow scorpion Tityus serrulatus, mainly focusing in the initial protein digestion. The transcriptome generated database allowed the quantitative identification by mass spectrometry of different enzymes and proteins involved in digestion. All the results suggested that cysteine cathepsins play an important role in protein digestion. Two digestive cysteine cathepsins were isolated and characterized presenting acidic characteristics (pH optima and stability), zymogen conversion to the mature form after acidic activation and a cross-class inhibition by pepstatin. A more elucidative picture of the molecular mechanism of digestion in a scorpion was proposed based on our results from Tityus serrulatus. The midgut and midgut glands (MMG) are composed by secretory and digestive cells. In fasting animals, the secretory granules are ready for the next predation event, containing enzymes needed for alkaline extra-oral digestion which will compose the digestive fluid, such as trypsins, astacins and chitinase. The digestive vacuoles are filled with an acidic proteolytic cocktail to the intracellular digestion composed by cathepsins L, B, F, D and legumain. Other proteins as lipases, carbohydrases, ctenitoxins and a chitolectin with a perithrophin domain were also detected. Evolutionarily, a large gene duplication of cathepsin L occurred in Arachnida with the sequences from ticks being completely divergent from other arachnids probably due to the particular selective pressures over this group.

L. monocytogenes in a cheese processing facility: Learning from contamination scenarios over three years of sampling.

PubMed

Rückerl, I; Muhterem-Uyar, M; Muri-Klinger, S; Wagner, K-H; Wagner, M; Stessl, B

2014-10-17

The aim of this study was to analyze the changing patterns of Listeria monocytogenes contamination in a cheese processing facility manufacturing a wide range of ready-to-eat products. Characterization of L. monocytogenes isolates included genotyping by pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Disinfectant-susceptibility tests and the assessment of L. monocytogenes survival in fresh cheese were also conducted. During the sampling period between 2010 and 2013, a total of 1284 environmental samples were investigated. Overall occurrence rates of Listeria spp. and L. monocytogenes were 21.9% and 19.5%, respectively. Identical L. monocytogenes genotypes were found in the food processing environment (FPE), raw materials and in products. Interventions after the sampling events changed contamination scenarios substantially. The high diversity of globally, widely distributed L. monocytogenes genotypes was reduced by identifying the major sources of contamination. Although susceptible to a broad range of disinfectants and cleaners, one dominant L. monocytogenes sequence type (ST) 5 could not be eradicated from drains and floors. Significantly, intense humidity and steam could be observed in all rooms and water residues were visible on floors due to increased cleaning strategies. This could explain the high L. monocytogenes contamination of the FPE (drains, shoes and floors) throughout the study (15.8%). The outcome of a challenge experiment in fresh cheese showed that L. monocytogenes could survive after 14days of storage at insufficient cooling temperatures (8 and 16°C). All efforts to reduce L. monocytogenes environmental contamination eventually led to a transition from dynamic to stable contamination scenarios. Consequently, implementation of systematic environmental monitoring via in-house systems should either aim for total avoidance of FPE colonization, or emphasize a first reduction of L. monocytogenes to sites where contamination of the processed product is unlikely. Drying of surfaces after cleaning is highly recommended to facilitate the L. monocytogenes eradication. Copyright © 2014 Elsevier B.V. All rights reserved.

Electromagnetic emission experiences using electric propulsion systems: A survey

NASA Technical Reports Server (NTRS)

Sovey, James S.; Zana, Lynnette M.; Knowles, Steven C.

1987-01-01

As electric propulsion systems become ready to integrate with spacecraft systems, the impact of propulsion system radiated emissions are of significant interest. Radiated emissions from electromagnetic, electrostatic, and electrothermal systems have been characterized and results synopsized from the literature describing 21 space flight programs. Electromagnetic radiated emission results from ground tests and flight experiences are presented with particular attention paid to the performance of spacecraft subsystems and payloads during thruster operations. The impacts to transmission of radio frequency signals through plasma plumes are also reviewed.

SPROC: A multiple-processor DSP IC

NASA Technical Reports Server (NTRS)

Davis, R.

1991-01-01

A large, single-chip, multiple-processor, digital signal processing (DSP) integrated circuit (IC) fabricated in HP-Cmos34 is presented. The innovative architecture is best suited for analog and real-time systems characterized by both parallel signal data flows and concurrent logic processing. The IC is supported by a powerful development system that transforms graphical signal flow graphs into production-ready systems in minutes. Automatic compiler partitioning of tasks among four on-chip processors gives the IC the signal processing power of several conventional DSP chips.

Solid State Radiation Dosimeters for Space and Medical Applications

NASA Technical Reports Server (NTRS)

Buehler, Martin G. (Editor)

1996-01-01

This report describes the development of two radiation monitors (RADMON's) for use in detecting total radiation dose and high-energy particles. These radiation detectors are chip-size devices fabricated in 1.2 micrometer CMOS and have flown in space on both experimental and commercial spacecraft. They have been used to characterize protons and electrons in the Earth's radiation belts, particles from the Sun, and protons used for medical therapy. Having proven useful in a variety of applications, the detector is now being readied for commercialization.

Inter-cusp Ion and Electron Transport in a Nstar-derivative Ion Thruster

NASA Technical Reports Server (NTRS)

Foster, John E.

2001-01-01

Diffusion of electrons and ions to anode surfaces between the magnetic cusps of a NASA Solar Electric Propulsion Technology Application Readiness ion thruster has been characterized. Ion flux measurements were made at the anode and at the screen grid electrode. The measurements indicated that the average ion current density at the anode and at the screen grid were approximately equal. Additionally, it was found that the electron flux to the anode between cusps is best described by the classical cross-field diffusion coefficient.

Ion and Electron Transport in an Nstar-derivative Ion Thruster. Revised

NASA Technical Reports Server (NTRS)

Foster, John E.

2001-01-01

Diffusion of electrons and ions to anode surfaces between the magnetic cusps of a NASA Solar Electric Propulsion Technology Application Readiness ion thruster has been characterized. Ion flux measurements were made at the anode and at the screen grid electrode. The measurements indicated that the average ion current density at the anode and at the screen grid were approximately equal. Additionally, it was found that the electron flux to the anode between cusps is best described by the classical cross-field diffusion coefficient.

Isolation and characterization of major histocompatibility complex class II B genes in cranes.

PubMed

Kohyama, Tetsuo I; Akiyama, Takuya; Nishida, Chizuko; Takami, Kazutoshi; Onuma, Manabu; Momose, Kunikazu; Masuda, Ryuichi

2015-11-01

In this study, we isolated and characterized the major histocompatibility complex (MHC) class II B genes in cranes. Genomic sequences spanning exons 1 to 4 were amplified and determined in 13 crane species and three other species closely related to cranes. In all, 55 unique sequences were identified, and at least two polymorphic MHC class II B loci were found in most species. An analysis of sequence polymorphisms showed the signature of positive selection and recombination. A phylogenetic reconstruction based on exon 2 sequences indicated that trans-species polymorphism has persisted for at least 10 million years, whereas phylogenetic analyses of the sequences flanking exon 2 revealed a pattern of concerted evolution. These results suggest that both balancing selection and recombination play important roles in the crane MHC evolution.

Quantum-Sequencing: Biophysics of quantum tunneling through nucleic acids

NASA Astrophysics Data System (ADS)

Casamada Ribot, Josep; Chatterjee, Anushree; Nagpal, Prashant

2014-03-01

Tunneling microscopy and spectroscopy has extensively been used in physical surface sciences to study quantum tunneling to measure electronic local density of states of nanomaterials and to characterize adsorbed species. Quantum-Sequencing (Q-Seq) is a new method based on tunneling microscopy for electronic sequencing of single molecule of nucleic acids. A major goal of third-generation sequencing technologies is to develop a fast, reliable, enzyme-free single-molecule sequencing method. Here, we present the unique ``electronic fingerprints'' for all nucleotides on DNA and RNA using Q-Seq along their intrinsic biophysical parameters. We have analyzed tunneling spectra for the nucleotides at different pH conditions and analyzed the HOMO, LUMO and energy gap for all of them. In addition we show a number of biophysical parameters to further characterize all nucleobases (electron and hole transition voltage and energy barriers). These results highlight the robustness of Q-Seq as a technique for next-generation sequencing.

Rickettsia asembonensis Characterization by Multilocus Sequence Typing of Complete Genes, Peru.

PubMed

Loyola, Steev; Flores-Mendoza, Carmen; Torre, Armando; Kocher, Claudine; Melendrez, Melanie; Luce-Fedrow, Alison; Maina, Alice N; Richards, Allen L; Leguia, Mariana

2018-05-01

While studying rickettsial infections in Peru, we detected Rickettsia asembonensis in fleas from domestic animals. We characterized 5 complete genomic regions (17kDa, gltA, ompA, ompB, and sca4) and conducted multilocus sequence typing and phylogenetic analyses. The molecular isolate from Peru is distinct from the original R. asembonensis strain from Kenya.

A microfluidic device for preparing next generation DNA sequencing libraries and for automating other laboratory protocols that require one or more column chromatography steps.

PubMed

Tan, Swee Jin; Phan, Huan; Gerry, Benjamin Michael; Kuhn, Alexandre; Hong, Lewis Zuocheng; Min Ong, Yao; Poon, Polly Suk Yean; Unger, Marc Alexander; Jones, Robert C; Quake, Stephen R; Burkholder, William F

2013-01-01

Library preparation for next-generation DNA sequencing (NGS) remains a key bottleneck in the sequencing process which can be relieved through improved automation and miniaturization. We describe a microfluidic device for automating laboratory protocols that require one or more column chromatography steps and demonstrate its utility for preparing Next Generation sequencing libraries for the Illumina and Ion Torrent platforms. Sixteen different libraries can be generated simultaneously with significantly reduced reagent cost and hands-on time compared to manual library preparation. Using an appropriate column matrix and buffers, size selection can be performed on-chip following end-repair, dA tailing, and linker ligation, so that the libraries eluted from the chip are ready for sequencing. The core architecture of the device ensures uniform, reproducible column packing without user supervision and accommodates multiple routine protocol steps in any sequence, such as reagent mixing and incubation; column packing, loading, washing, elution, and regeneration; capture of eluted material for use as a substrate in a later step of the protocol; and removal of one column matrix so that two or more column matrices with different functional properties can be used in the same protocol. The microfluidic device is mounted on a plastic carrier so that reagents and products can be aliquoted and recovered using standard pipettors and liquid handling robots. The carrier-mounted device is operated using a benchtop controller that seals and operates the device with programmable temperature control, eliminating any requirement for the user to manually attach tubing or connectors. In addition to NGS library preparation, the device and controller are suitable for automating other time-consuming and error-prone laboratory protocols requiring column chromatography steps, such as chromatin immunoprecipitation.

A Microfluidic Device for Preparing Next Generation DNA Sequencing Libraries and for Automating Other Laboratory Protocols That Require One or More Column Chromatography Steps

PubMed Central

Tan, Swee Jin; Phan, Huan; Gerry, Benjamin Michael; Kuhn, Alexandre; Hong, Lewis Zuocheng; Min Ong, Yao; Poon, Polly Suk Yean; Unger, Marc Alexander; Jones, Robert C.; Quake, Stephen R.; Burkholder, William F.

2013-01-01

Library preparation for next-generation DNA sequencing (NGS) remains a key bottleneck in the sequencing process which can be relieved through improved automation and miniaturization. We describe a microfluidic device for automating laboratory protocols that require one or more column chromatography steps and demonstrate its utility for preparing Next Generation sequencing libraries for the Illumina and Ion Torrent platforms. Sixteen different libraries can be generated simultaneously with significantly reduced reagent cost and hands-on time compared to manual library preparation. Using an appropriate column matrix and buffers, size selection can be performed on-chip following end-repair, dA tailing, and linker ligation, so that the libraries eluted from the chip are ready for sequencing. The core architecture of the device ensures uniform, reproducible column packing without user supervision and accommodates multiple routine protocol steps in any sequence, such as reagent mixing and incubation; column packing, loading, washing, elution, and regeneration; capture of eluted material for use as a substrate in a later step of the protocol; and removal of one column matrix so that two or more column matrices with different functional properties can be used in the same protocol. The microfluidic device is mounted on a plastic carrier so that reagents and products can be aliquoted and recovered using standard pipettors and liquid handling robots. The carrier-mounted device is operated using a benchtop controller that seals and operates the device with programmable temperature control, eliminating any requirement for the user to manually attach tubing or connectors. In addition to NGS library preparation, the device and controller are suitable for automating other time-consuming and error-prone laboratory protocols requiring column chromatography steps, such as chromatin immunoprecipitation. PMID:23894273

Next-generation sequencing of the BRCA1 and BRCA2 genes for the genetic diagnostics of hereditary breast and/or ovarian cancer.

PubMed

Trujillano, Daniel; Weiss, Maximilian E R; Schneider, Juliane; Köster, Julia; Papachristos, Efstathios B; Saviouk, Viatcheslav; Zakharkina, Tetyana; Nahavandi, Nahid; Kovacevic, Lejla; Rolfs, Arndt

2015-03-01

Genetic testing for hereditary breast and/or ovarian cancer mostly relies on laborious molecular tools that use Sanger sequencing to scan for mutations in the BRCA1 and BRCA2 genes. We explored a more efficient genetic screening strategy based on next-generation sequencing of the BRCA1 and BRCA2 genes in 210 hereditary breast and/or ovarian cancer patients. We first validated this approach in a cohort of 115 samples with previously known BRCA1 and BRCA2 mutations and polymorphisms. Genomic DNA was amplified using the Ion AmpliSeq BRCA1 and BRCA2 panel. The DNA Libraries were pooled, barcoded, and sequenced using an Ion Torrent Personal Genome Machine sequencer. The combination of different robust bioinformatics tools allowed detection of all previously known pathogenic mutations and polymorphisms in the 115 samples, without detecting spurious pathogenic calls. We then used the same assay in a discovery cohort of 95 uncharacterized hereditary breast and/or ovarian cancer patients for BRCA1 and BRCA2. In addition, we describe the allelic frequencies across 210 hereditary breast and/or ovarian cancer patients of 74 unique definitely and likely pathogenic and uncertain BRCA1 and BRCA2 variants, some of which have not been previously annotated in the public databases. Targeted next-generation sequencing is ready to substitute classic molecular methods to perform genetic testing on the BRCA1 and BRCA2 genes and provides a greater opportunity for more comprehensive testing of at-risk patients. Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

The genetic-environmental etiology of cognitive school readiness and later academic achievement in early childhood.

PubMed

Lemelin, Jean-Pascal; Boivin, Michel; Forget-Dubois, Nadine; Dionne, Ginette; Séguin, Jean R; Brendgen, Mara; Vitaro, Frank; Tremblay, Richard E; Pérusse, Daniel

2007-01-01

Using a genetic design of 840 60-month-old twins, this study investigated the genetic and environmental contributions to (a) individual differences in four components of cognitive school readiness, (b) the general ability underlying these four components, and (c) the predictive association between school readiness and school achievement. Results revealed that the contribution of the shared environment for cognitive school readiness was substantial. Genetic effects were more important for the core abilities underlying school readiness than for each specific skill, although shared environment remained the largest factor overall. Genetic, shared, and nonshared environmental factors all accounted for the predictive association between school readiness and early school achievement. These results contribute to a better understanding of the early determinants of school readiness.

Population-Sequencing as a Biomarker of Burkholderia mallei and Burkholderia pseudomallei Evolution through Microbial Forensic Analysis.

PubMed

Jakupciak, John P; Wells, Jeffrey M; Karalus, Richard J; Pawlowski, David R; Lin, Jeffrey S; Feldman, Andrew B

2013-01-01

Large-scale genomics projects are identifying biomarkers to detect human disease. B. pseudomallei and B. mallei are two closely related select agents that cause melioidosis and glanders. Accurate characterization of metagenomic samples is dependent on accurate measurements of genetic variation between isolates with resolution down to strain level. Often single biomarker sensitivity is augmented by use of multiple or panels of biomarkers. In parallel with single biomarker validation, advances in DNA sequencing enable analysis of entire genomes in a single run: population-sequencing. Potentially, direct sequencing could be used to analyze an entire genome to serve as the biomarker for genome identification. However, genome variation and population diversity complicate use of direct sequencing, as well as differences caused by sample preparation protocols including sequencing artifacts and mistakes. As part of a Department of Homeland Security program in bacterial forensics, we examined how to implement whole genome sequencing (WGS) analysis as a judicially defensible forensic method for attributing microbial sample relatedness; and also to determine the strengths and limitations of whole genome sequence analysis in a forensics context. Herein, we demonstrate use of sequencing to provide genetic characterization of populations: direct sequencing of populations.

Population-Sequencing as a Biomarker of Burkholderia mallei and Burkholderia pseudomallei Evolution through Microbial Forensic Analysis

PubMed Central

Jakupciak, John P.; Wells, Jeffrey M.; Karalus, Richard J.; Pawlowski, David R.; Lin, Jeffrey S.; Feldman, Andrew B.

2013-01-01

Large-scale genomics projects are identifying biomarkers to detect human disease. B. pseudomallei and B. mallei are two closely related select agents that cause melioidosis and glanders. Accurate characterization of metagenomic samples is dependent on accurate measurements of genetic variation between isolates with resolution down to strain level. Often single biomarker sensitivity is augmented by use of multiple or panels of biomarkers. In parallel with single biomarker validation, advances in DNA sequencing enable analysis of entire genomes in a single run: population-sequencing. Potentially, direct sequencing could be used to analyze an entire genome to serve as the biomarker for genome identification. However, genome variation and population diversity complicate use of direct sequencing, as well as differences caused by sample preparation protocols including sequencing artifacts and mistakes. As part of a Department of Homeland Security program in bacterial forensics, we examined how to implement whole genome sequencing (WGS) analysis as a judicially defensible forensic method for attributing microbial sample relatedness; and also to determine the strengths and limitations of whole genome sequence analysis in a forensics context. Herein, we demonstrate use of sequencing to provide genetic characterization of populations: direct sequencing of populations. PMID:24455204

A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae)

PubMed Central

Tank, David C.

2016-01-01

Advances in high-throughput sequencing (HTS) have allowed researchers to obtain large amounts of biological sequence information at speeds and costs unimaginable only a decade ago. Phylogenetics, and the study of evolution in general, is quickly migrating towards using HTS to generate larger and more complex molecular datasets. In this paper, we present a method that utilizes microfluidic PCR and HTS to generate large amounts of sequence data suitable for phylogenetic analyses. The approach uses the Fluidigm Access Array System (Fluidigm, San Francisco, CA, USA) and two sets of PCR primers to simultaneously amplify 48 target regions across 48 samples, incorporating sample-specific barcodes and HTS adapters (2,304 unique amplicons per Access Array). The final product is a pooled set of amplicons ready to be sequenced, and thus, there is no need to construct separate, costly genomic libraries for each sample. Further, we present a bioinformatics pipeline to process the raw HTS reads to either generate consensus sequences (with or without ambiguities) for every locus in every sample or—more importantly—recover the separate alleles from heterozygous target regions in each sample. This is important because it adds allelic information that is well suited for coalescent-based phylogenetic analyses that are becoming very common in conservation and evolutionary biology. To test our approach and bioinformatics pipeline, we sequenced 576 samples across 96 target regions belonging to the South American clade of the genus Bartsia L. in the plant family Orobanchaceae. After sequencing cleanup and alignment, the experiment resulted in ~25,300bp across 486 samples for a set of 48 primer pairs targeting the plastome, and ~13,500bp for 363 samples for a set of primers targeting regions in the nuclear genome. Finally, we constructed a combined concatenated matrix from all 96 primer combinations, resulting in a combined aligned length of ~40,500bp for 349 samples. PMID:26828929

Investigation of SnSPR1, a novel and abundant surface protein of Sarcocystis neurona merozoites.

PubMed

Zhang, Deqing; Howe, Daniel K

2008-04-15

An expressed sequence tag (EST) sequencing project has produced over 15,000 partial cDNA sequences from the equine pathogen Sarcocystis neurona. While many of the sequences are clear homologues of previously characterized genes, a significant number of the S. neurona ESTs do not exhibit similarity to anything in the extensive sequence databases that have been generated. In an effort to characterize parasite proteins that are novel to S. neurona, a seemingly unique gene was selected for further investigation based on its abundant representation in the collection of ESTs and the predicted presence of a signal peptide and glycolipid anchor addition on the encoded protein. The gene was expressed in E. coli, and monospecific polyclonal antiserum against the recombinant protein was produced by immunization of a rabbit. Characterization of the native protein in S. neurona merozoites and schizonts revealed that it is a low molecular weight surface protein that is expressed throughout intracellular development of the parasite. The protein was designated Surface Protein 1 (SPR1) to reflect its display on the outer surface of merozoites and to distinguish it from the ubiquitous SAG/SRS surface antigens of the heteroxenous Coccidia. Interestingly, infection assays in the presence of the polyclonal antiserum suggested that SnSPR1 plays some role in attachment and/or invasion of host cells by S. neurona merozoites. The work described herein represents a general template for selecting and characterizing the various unidentified gene sequences that are plentiful in the EST databases for S. neurona and other apicomplexans. Furthermore, this study illustrates the value of investigating these novel sequences since it can offer new candidates for diagnostic or vaccine development while also providing greater insight into the biology of these parasites.

Neural Encoding and Integration of Learned Probabilistic Sequences in Avian Sensory-Motor Circuitry

PubMed Central

Brainard, Michael S.

2013-01-01

Many complex behaviors, such as human speech and birdsong, reflect a set of categorical actions that can be flexibly organized into variable sequences. However, little is known about how the brain encodes the probabilities of such sequences. Behavioral sequences are typically characterized by the probability of transitioning from a given action to any subsequent action (which we term “divergence probability”). In contrast, we hypothesized that neural circuits might encode the probability of transitioning to a given action from any preceding action (which we term “convergence probability”). The convergence probability of repeatedly experienced sequences could naturally become encoded by Hebbian plasticity operating on the patterns of neural activity associated with those sequences. To determine whether convergence probability is encoded in the nervous system, we investigated how auditory-motor neurons in vocal premotor nucleus HVC of songbirds encode different probabilistic characterizations of produced syllable sequences. We recorded responses to auditory playback of pseudorandomly sequenced syllables from the bird's repertoire, and found that variations in responses to a given syllable could be explained by a positive linear dependence on the convergence probability of preceding sequences. Furthermore, convergence probability accounted for more response variation than other probabilistic characterizations, including divergence probability. Finally, we found that responses integrated over >7–10 syllables (∼700–1000 ms) with the sign, gain, and temporal extent of integration depending on convergence probability. Our results demonstrate that convergence probability is encoded in sensory-motor circuitry of the song-system, and suggest that encoding of convergence probability is a general feature of sensory-motor circuits. PMID:24198363

Beyond signal functions in global obstetric care: Using a clinical cascade to measure emergency obstetric readiness

PubMed Central

Dettinger, Julia; Calkins, Kimberly; Kibore, Minnie; Gachuno, Onesmus; Walker, Dilys

2018-01-01

Background Globally, the rate of reduction in delivery-associated maternal and perinatal mortality has been slow compared to improvements in post-delivery mortality in children under five. Improving clinical readiness for basic obstetric emergencies is crucial for reducing facility-based maternal deaths. Emergency readiness is commonly assessed using tracers derived from the maternal signal functions model. Objective-method We compare emergency readiness using the signal functions model and a novel clinical cascade. The cascades model readiness as the proportion of facilities with resources to identify the emergency (stage 1), treat it (stage 2) and monitor-modify therapy (stage 3). Data were collected from 44 Kenyan clinics as part of an implementation trial. Findings Although most facilities (77.0%) stock maternal signal function tracer drugs, far fewer have resources to practically identify and treat emergencies. In hypertensive emergencies for example, 38.6% of facilities have resources to identify the emergency (Stage 1 readiness, including sphygmomanometer, stethoscope, urine collection device, protein test). 6.8% have the resources to treat the emergency (Stage 2, consumables (IV Kit, fluids), durable goods (IV pole) and drugs (magnesium sulfate and hydralazine). No facilities could monitor or modify therapy (Stage 3). Across five maternal emergencies, the signal functions overestimate readiness by 54.5%. A consistent, step-wise pattern of readiness loss across signal functions and care stage emerged and was profoundly consistent at 33.0%. Significance Comparing estimates from the maternal signal functions and cascades illustrates four themes. First, signal functions overestimate practical readiness by 55%. Second, the cascade’s intuitive indicators can support cross-sector health system or program planners to more precisely measure and improve emergency care. Third, adding few variables to existing readiness inventories permits step-wise modeling of readiness loss and can inform more precise interventions. Fourth, the novel aggregate readiness loss indicator provides an innovative and intuitive approach for modeling health system emergency readiness. Additional testing in diverse contexts is warranted. PMID:29474397

Using the structure-function linkage database to characterize functional domains in enzymes.

PubMed

Brown, Shoshana; Babbitt, Patricia

2014-12-12

The Structure-Function Linkage Database (SFLD; http://sfld.rbvi.ucsf.edu/) is a Web-accessible database designed to link enzyme sequence, structure, and functional information. This unit describes the protocols by which a user may query the database to predict the function of uncharacterized enzymes and to correct misannotated functional assignments. The information in this unit is especially useful in helping a user discriminate functional capabilities of a sequence that is only distantly related to characterized sequences in publicly available databases. Copyright © 2014 John Wiley & Sons, Inc.

Television Viewing, Educational Quality of the Home Environment, and School Readiness.

ERIC Educational Resources Information Center

Clarke, Angela Teresa; Kurtz-Costes, Beth

1997-01-01

Researchers examined relationships among children's television viewing, school readiness, parental employment, and the home environment's educational quality. Thirty low-income parents completed surveys. Their preschoolers completed IQ and school readiness assessments. Television viewing adversely related to school readiness and the home…

Detection and characterization of Shiga toxin-producing Escherichia coli in game meat and ready-to-eat meat products.

PubMed

Díaz-Sánchez, S; Sánchez, S; Sánchez, M; Herrera-León, S; Hanning, I; Vidal, D

2012-11-15

A total of 142 samples of game meat and ready-to-eat meat products from red deer and wild boar were analysed in order to assess the presence of Shiga toxin-producing Escherichia coli (STEC). Shiga-toxin encoding genes (stx genes) were detected by PCR in 36 (25.4%) of the samples and STEC was isolated from 8 (5.6%) of the same samples. None of the samples tested positive for E. coli O157:H7. Four different serotypes were found among the 8 STEC isolates, with serotype O27:H30 being predominant (62.5%, 5/8). The PCR assay indicated the presence of the stx2 gene in all of the STEC isolates and further subtyping resulted in detection of three different subtypes: stx2a, stx2b and stx2g. The only stx1-positive isolate was further subtyped as stx1c. The ehxA gene was detected in 3 (37.5%) of the isolates and none of them contained the eae gene. All STEC isolates were sensitive to the 13 antibiotics tested. Some isolates possessed serotypes and virulence gene profiles previously associated with STEC infections in humans. The isolation of a STEC strain carrying the stx2a subtype from a ready-to-eat meat product from deer suggests the role of these products as a potential source of STEC infections in humans. Copyright © 2012 Elsevier B.V. All rights reserved.

The impact of fashion competence and achievement motivation toward college student’s working readiness on “Cipta Karya” subject

NASA Astrophysics Data System (ADS)

Marniati; Wibawa, S. C.

2018-01-01

This experiment aimed to know the rate of college student’s working readiness of fashion’s program study to perform ‘Cipta Karya’ related to cognitive readiness, manner readiness and skill readiness from a variable of fashion’s workmanship and achievement motivation. The subject of the experiment was 43 college students who took Cipta Karya subject. Method of collecting data used questionnaire with five alternative answers to Likert ratio model. Data analysis technique used path analysis (double regression). The instrument validity test used product moment correlation while for instrument reliability used Alpha Cronbach’s grade. The results showed (1) fashion competence was taking effect significantly on working readiness for ‘Cipta Karya’ (2) achievement motivation is taking effect significantly on working readiness for ‘cipta karya’ (3) both variables are positive. This means that fashion competence and achievement motivation have a positive effect on working readiness for ‘cipta karya’ performance.

Sharing leadership influence: a life-cycle model.

PubMed

Hunt, E H; Sleeth, R G

1977-07-01

We have described the effective leader in terms of several concepts: (1) leadership style as a means of sharing the influence of leadership with a ready group; (2) the readiness of a group to successfully exert influence on the practice; (3) the matching of leadership styles with group readiness; and (4) the impact of the environment on the readiness of a group. We have described how all of these elements combine to determine a leader's effectiveness. All elements interact and present the leader with a situation for which he must adopt an appropriate leadership style (Table 1). Several elements combine to change the readiness of a group through four phases - unready, ready, mature, and professional. The leader then matches leadership styles I through IV to these levels of readiness. We believe a dentist will be effective as a leader in proportion to his success in matching an appropriate leadership style to the readiness of his group to perform in its particular environment.

Tracking of Listeria monocytogenes in meat establishment using Whole Genome Sequencing as a food safety management tool: A proof of concept.

PubMed

Nastasijevic, Ivan; Milanov, Dubravka; Velebit, Branko; Djordjevic, Vesna; Swift, Craig; Painset, Anais; Lakicevic, Brankica

2017-09-18

Repeated Listeria outbreaks particularly associated with Ready-To-Eat (RTE) delicatessen meat products have been reported annually at global level. The most frequent scenario that led to foodborne outbreaks was the post-thermal treatment cross-contamination of deli meat products during slicing and modified atmosphere packaging (MAP). The precondition for such cross contamination is the previous introduction of Listeria into meat processing facilities and subsequent colonization of the production environment, associated with formation of biofilms resilient to common sanitation procedures regularly applied in meat establishments. The use of Whole Genome Sequencing (WGS) can facilitate the understanding of contamination and colonization routes of pathogens within the food production environment and enable efficient pathogen tracking among different departments. This study aimed to: a) provide a proof of concept on practical use of WGS in a meat establishment to define the entry routes and spread pattern of L. monocytogenes, and b) to consider the regular use of WGS in meat processing establishments as a strong support of food safety management system. The results revealed that Listeria spp. was present in slaughter line, chilling chambers, deboning, slicing, MAP, as well as in corridors and dispatch (53 positive samples, out of 240). Eight L. monocytogenes isolates (out of 53) were identified from the slaughterhouse, chilling chambers, deboning, MAP and dispatch. L. monocytogenes isolates were of three different serotypes (1/2a, 1/2c, 4b) and correspondingly of three MLST sequence types. Overall, two pairs of L. monocytogenes isolates were genetically identical, i.e. two serotype 4b isolates (ST1), isolated from water drain at dispatch unit and two isolates obtained from slaughterhouse (floorwall junction at the carcass wash point) and MAP (water drain). These findings indicated that L. monocytogenes isolates identified in meat processing units (MAP, chilling chamber and dispatch) originated from the slaughter line. Further, all eight L. monocytogenes isolates were confirmed to be biofilm producers on glass and stainless steel surfaces. The identification of the main entry routes of L. monocytogenes into meat establishments and tracking the routes for spread of the pathogen are of essential importance to define appropriate risk mitigation strategies for L. monocytogenes in meat production environment. The routine use of WGS for bacterial characterization, as a strong support of food safety management system in meat establishments, will require the cost-effective approach. It may encompass in-house sequencing when sequencing equipment is used for multiple applications (e.g. WGS of pathogens, starter cultures and spoilage organisms). Copyright © 2017 Elsevier B.V. All rights reserved.

Detection and characterization of hepatitis A virus circulating in Egypt.

PubMed

Hamza, Hazem; Abd-Elshafy, Dina Nadeem; Fayed, Sayed A; Bahgat, Mahmoud Mohamed; El-Esnawy, Nagwa Abass; Abdel-Mobdy, Emam

2017-07-01

Hepatitis A virus (HAV) still poses a considerable problem worldwide. In the current study, hepatitis A virus was recovered from wastewater samples collected from three wastewater treatment plants over one year. Using RT-PCR, HAV was detected in 43 out of 68 samples (63.2%) representing both inlet and outlet. Eleven positive samples were subjected to sequencing targeting the VP1-2A junction region. Phylogenetic analysis revealed that all samples belonged to subgenotype IB with few substitutions at the amino acid level. The complete sequence of one isolate (HAV/Egy/BI-11/2015) showed that the similarity at the amino acid level was not reflected at the nucleotide level. However, the deduced amino acid sequence derived from the complete nucleotide sequence showed distinct substitutions in the 2B, 2C, and 3A regions. Recombination analysis revealed a recombination event between X75215 (subgenotype IA) and AF268396 (subgenotype IB) involving a portion of the 2B nonstructural protein coding region (nucleotides 3757-3868) assuming the herein characterized sequence an actual recombinant. Despite the role of recombination in picornaviruses evolution, its involvement in HAV evolution has rarely been reported, and this may be due to the limited available complete HAV sequences. To our knowledge, this represents the first characterized complete sequence of an Egyptian isolate and the described recombination event provides an important update on the circulating HAV strains in Egypt.

Measures of readiness for cognitive behavioural therapy in people with intellectual disability: A systematic review.

PubMed

Stott, Joshua; Charlesworth, Georgina; Scior, Katrina

2017-01-01

Cognitive behavioural therapy (CBT) is a promising treatment for mental health problems in people with intellectual disabilities but some may not be suited or ready. This review critically evaluates the quality and utility of measures of CBT readiness in people with intellectual disabilities. Twelve studies of six measures based on three aspects of CBT readiness were identified through systematic review. Across measures, measurement quality was largely poor or un-assessed. Only one study evaluated measurement change over the course of CBT. Not all participants with intellectual disabilities could 'pass' readiness measures and performance may be affected by levels of language and cognitive functioning. There was some evidence that CBT readiness is trainable with brief interventions. Before using readiness measures in a clinical context, further work is needed to extend initial evidence on recognising cognitive mediation as a CBT readiness ability. Given the lack of consensus as to the definition of CBT readiness and the heterogeneity of CBT interventions, future research could also focus on developing readiness measures using a bottom up approach, developing measures within the context of CBT interventions themselves, before further refining and establishing their psychometric properties. This paper is the first to systematically review measures of skills thought necessary to be ready for cognitive behavioural therapy in intellectual disabilities. The findings suggest that while readiness skills may be trainable with brief interventions, the available measures of these skills have not been fully evaluated for quality. Levels of functioning on these measures have yet to be established relative to those without intellectual disabilities and critically, there is very little evidence as to whether these skills are important in cognitive behavioural therapy process and outcome. We suggest that future research could focus on those constructs where there is preliminary evidence for utility such as recognising cognitive mediation and also on developing the concept of readiness perhaps by developing measures within the context of specific CBT interventions. Until this is done, clinicians should exercise caution in using these measures to assess readiness for cognitive behavioural therapy in people with intellectual disabilities. Copyright © 2016 Elsevier Ltd. All rights reserved.

Research on Influencing Factors of Salespeople's Empowerment Readiness in Green Energy Enterprise

NASA Astrophysics Data System (ADS)

Dong, Yuan; Liu, Xiaohui

As market competition in green energy enterprises continues to intensify, marketing activities are enlarging and customer demand is increasingly growing and diversifying. More and more green energy enterprises have empowered their own salespeople. And managers in green energy enterprises are more concerned with the issues which employees suit to be empowered and which factors will influence employee empowerment readiness. This paper proposes the definition of salespeople's empowerment readiness, analyzes influencing factors of salespeople's empowerment readiness, discusses the effect mechanism of influencing factors of salespeople's empowerment readiness, finally, and puts forward some suggestions to enhance salespeople's empowerment readiness from the perspective of human resource management practice.

Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database

PubMed Central

2011-01-01

Background The genus Silene is widely used as a model system for addressing ecological and evolutionary questions in plants, but advances in using the genus as a model system are impeded by the lack of available resources for studying its genome. Massively parallel sequencing cDNA has recently developed into an efficient method for characterizing the transcriptomes of non-model organisms, generating massive amounts of data that enable the study of multiple species in a comparative framework. The sequences generated provide an excellent resource for identifying expressed genes, characterizing functional variation and developing molecular markers, thereby laying the foundations for future studies on gene sequence and gene expression divergence. Here, we report the results of a comparative transcriptome sequencing study of eight individuals representing four Silene and one Dianthus species as outgroup. All sequences and annotations have been deposited in a newly developed and publicly available database called SiESTa, the Silene EST annotation database. Results A total of 1,041,122 EST reads were generated in two runs on a Roche GS-FLX 454 pyrosequencing platform. EST reads were analyzed separately for all eight individuals sequenced and were assembled into contigs using TGICL. These were annotated with results from BLASTX searches and Gene Ontology (GO) terms, and thousands of single-nucleotide polymorphisms (SNPs) were characterized. Unassembled reads were kept as singletons and together with the contigs contributed to the unigenes characterized in each individual. The high quality of unigenes is evidenced by the proportion (49%) that have significant hits in similarity searches with the A. thaliana proteome. The SiESTa database is accessible at http://www.siesta.ethz.ch. Conclusion The sequence collections established in the present study provide an important genomic resource for four Silene and one Dianthus species and will help to further develop Silene as a plant model system. The genes characterized will be useful for future research not only in the species included in the present study, but also in related species for which no genomic resources are yet available. Our results demonstrate the efficiency of massively parallel transcriptome sequencing in a comparative framework as an approach for developing genomic resources in diverse groups of non-model organisms. PMID:21791039

Genome editing with CompoZr custom zinc finger nucleases (ZFNs).

PubMed

Hansen, Keith; Coussens, Matthew J; Sago, Jack; Subramanian, Shilpi; Gjoka, Monika; Briner, Dave

2012-06-14

Genome editing is a powerful technique that can be used to elucidate gene function and the genetic basis of disease. Traditional gene editing methods such as chemical-based mutagenesis or random integration of DNA sequences confer indiscriminate genetic changes in an overall inefficient manner and require incorporation of undesirable synthetic sequences or use of aberrant culture conditions, potentially confusing biological study. By contrast, transient ZFN expression in a cell can facilitate precise, heritable gene editing in a highly efficient manner without the need for administration of chemicals or integration of synthetic transgenes. Zinc finger nucleases (ZFNs) are enzymes which bind and cut distinct sequences of double-stranded DNA (dsDNA). A functional CompoZr ZFN unit consists of two individual monomeric proteins that bind a DNA "half-site" of approximately 15-18 nucleotides (see Figure 1). When two ZFN monomers "home" to their adjacent target sites the DNA-cleavage domains dimerize and create a double-strand break (DSB) in the DNA. Introduction of ZFN-mediated DSBs in the genome lays a foundation for highly efficient genome editing. Imperfect repair of DSBs in a cell via the non-homologous end-joining (NHEJ) DNA repair pathway can result in small insertions and deletions (indels). Creation of indels within the gene coding sequence of a cell can result in frameshift and subsequent functional knockout of a gene locus at high efficiency. While this protocol describes the use of ZFNs to create a gene knockout, integration of transgenes may also be conducted via homology-directed repair at the ZFN cut site. The CompoZr Custom ZFN Service represents a systematic, comprehensive, and well-characterized approach to targeted gene editing for the scientific community with ZFN technology. Sigma scientists work closely with investigators to 1) perform due diligence analysis including analysis of relevant gene structure, biology, and model system pursuant to the project goals, 2) apply this knowledge to develop a sound targeting strategy, 3) then design, build, and functionally validate ZFNs for activity in a relevant cell line. The investigator receives positive control genomic DNA and primers, and ready-to-use ZFN reagents supplied in both plasmid DNA and in-vitro transcribed mRNA format. These reagents may then be delivered for transient expression in the investigator's cell line or cell type of choice. Samples are then tested for gene editing at the locus of interest by standard molecular biology techniques including PCR amplification, enzymatic digest, and electrophoresis. After positive signal for gene editing is detected in the initial population, cells are single-cell cloned and genotyped for identification of mutant clones/alleles.

Memory as embodiment: The case of modality and serial short-term memory.

PubMed

Macken, Bill; Taylor, John C; Kozlov, Michail D; Hughes, Robert W; Jones, Dylan M

2016-10-01

Classical explanations for the modality effect-superior short-term serial recall of auditory compared to visual sequences-typically recur to privileged processing of information derived from auditory sources. Here we critically appraise such accounts, and re-evaluate the nature of the canonical empirical phenomena that have motivated them. Three experiments show that the standard account of modality in memory is untenable, since auditory superiority in recency is often accompanied by visual superiority in mid-list serial positions. We explain this simultaneous auditory and visual superiority by reference to the way in which perceptual objects are formed in the two modalities and how those objects are mapped to speech motor forms to support sequence maintenance and reproduction. Specifically, stronger obligatory object formation operating in the standard auditory form of sequence presentation compared to that for visual sequences leads both to enhanced addressability of information at the object boundaries and reduced addressability for that in the interior. Because standard visual presentation does not lead to such object formation, such sequences do not show the boundary advantage observed for auditory presentation, but neither do they suffer loss of addressability associated with object information, thereby affording more ready mapping of that information into a rehearsal cohort to support recall. We show that a range of factors that impede this perceptual-motor mapping eliminate visual superiority while leaving auditory superiority unaffected. We make a general case for viewing short-term memory as an embodied, perceptual-motor process. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Wyoming Early Childhood Readiness Standards.

ERIC Educational Resources Information Center

Wyoming State Dept. of Education, Cheyenne.

Because children entering kindergarten come with a variety of preschool and home experiences, and accordingly, with varying levels of school readiness, the Wyoming Early Childhood Readiness Standards have been developed to provide a more consistent definition of school readiness. The goal for the Standards is to provide early childhood educators…

The Condition of College Readiness, 2009

ERIC Educational Resources Information Center

ACT, Inc., 2009

2009-01-01

Since 1959, ACT has collected and reported data on students' academic readiness for college. Because becoming ready for college is a process that occurs throughout elementary and secondary education, measuring academic performance over time in the context of college readiness provides meaningful and compelling information about the college…

Instructional Alignment of Workplace Readiness Skills in Marketing Education

ERIC Educational Resources Information Center

Martin, Sarah J.; Reed, Philip A.

2015-01-01

This study examined high school marketing education teachers' knowledge of workplace readiness skills and whether that knowledge had an impact on student workplace readiness skill achievement. Further, this study examined the usage of Virginia's 13 Workplace Readiness Skills curriculum and identified the teaching methods and instructional…

Characterization and complete genome sequence of a previously uncharacterized panicovirus from Bermuda grass detected by high throughput sequencing

USDA-ARS?s Scientific Manuscript database

Bermuda grass samples were examined by transmission electron microscopy and 28-30 nm spherical virus particles were observed. Total RNA from these plants was subjected to high throughput sequencing (HTS). The nearly full genome sequence of a previously uncharacterized Panicovirus was identified from...

Soldier Quality of Life (Operational) and Readiness at Contingency Base Camps: Insights From Qualitative Interviews

DTIC Science & Technology

2017-03-13

camps and Soldier/small unit readiness to guide the development of a quantitative readiness survey . • During structured interviews, 31 Soldiers...camps and Soldier/small unit readiness to guide the development of a quantitative readiness survey . 11UNCLASSIFIED Click to hear quote Methods...We were rock stars.” 60UNCLASSIFIED • These data are driving the selection of attributes for a future quantitative survey of the link between QoL

Molecular Characterization of Epiphytic Bacterial Communities on Charophycean Green Algae

PubMed Central

Fisher, Madeline M.; Wilcox, Lee W.; Graham, Linda E.

1998-01-01

Epiphytic bacterial communities within the sheath material of three filamentous green algae, Desmidium grevillii, Hyalotheca dissiliens, and Spondylosium pulchrum (class Charophyceae, order Zygnematales), collected from a Sphagnum bog were characterized by PCR amplification, cloning, and sequencing of 16S ribosomal DNA. A total of 20 partial sequences and nine different sequence types were obtained, and one sequence type was recovered from the bacterial communities on all three algae. By phylogenetic analysis, the cloned sequences were placed into several major lineages of the Bacteria domain: the Flexibacter/Cytophaga/Bacteroides phylum and the α, β, and γ subdivisions of the phylum Proteobacteria. Analysis at the subphylum level revealed that the majority of our sequences were not closely affiliated with those of known, cultured taxa, although the estimated evolutionary distances between our sequences and their nearest neighbors were always less than 0.1 (i.e., greater than 90% similar). This result suggests that the majority of sequences obtained in this study represent as yet phenotypically undescribed bacterial species and that the range of bacterial-algal interactions that occur in nature has not yet been fully described. PMID:9797295

SaludABLEOmaha: improving readiness to address obesity through healthy lifestyle in a Midwestern Latino community, 2011-2013.

PubMed

Frerichs, Leah; Brittin, Jeri; Robbins, Regina; Steenson, Sharalyn; Stewart, Catherine; Fisher, Christopher; Huang, Terry T-K

2015-02-12

A community's readiness for change is a precursor to the effective application of evidence-based practices for health promotion. Research is lacking regarding potential strategies to improve readiness to address obesity-related health issues in underserved communities. This case study describes SaludABLEOmaha, an initiative to increase readiness of residents in a Midwestern Latino community to address obesity and adopt healthy lifestyles. SaludABLEOmaha emphasized 2 core approaches, youth activism and collaboration among public and private institutions, which we applied to planning and implementing tactics in support of 3 interconnected strategies: 1) social marketing and social media, 2) service learning in schools (ie, curricula that integrate hands-on community service with instruction and reflection), and 3) community and business engagement. Following the Community Readiness Model protocol (http://triethniccenter.colostate.edu/communityReadiness.htm), structured interviews were conducted with community leaders and analyzed before and 2.5 years after launch of the program. The community increased in readiness from stage 3 of the Community Readiness Model, "vague awareness," at baseline to stage 5, "preparation," at follow-up. SaludABLEOmaha improved community readiness (eg, community knowledge, community climate), which probably contributed to the observed increase in readiness to address obesity through healthy lifestyle. Community mobilization approaches such as youth activism integrated with social marketing and social media tactics can improve community responsiveness to obesity prevention and diminish health disparities.

Readiness of communities to engage with childhood obesity prevention initiatives in disadvantaged areas of Victoria, Australia.

PubMed

Cyril, Sheila; Polonsky, Michael; Green, Julie; Agho, Kingsley; Renzaho, Andre

2017-07-01

Objective Disadvantaged communities bear a disproportionate burden of childhood obesity and show low participation in childhood obesity prevention initiatives. This study aims to examine the level of readiness of disadvantaged communities to engage with childhood obesity prevention initiatives. Methods Using the community readiness model, 95 semi-structured interviews were conducted among communities in four disadvantaged areas of Victoria, Australia. Community readiness analysis and paired t-tests were performed to assess the readiness levels of disadvantaged communities to engage with childhood obesity prevention initiatives. Results The results showed that disadvantaged communities demonstrated low levels of readiness (readiness score=4/9, 44%) to engage with the existing childhood obesity prevention initiatives, lacked knowledge of childhood obesity and its prevention, and reported facing challenges in initiating and sustaining participation in obesity prevention initiatives. Conclusion This study highlights the need to improve community readiness by addressing low obesity-related literacy levels among disadvantaged communities and by facilitating the capacity-building of bicultural workers to deliver obesity prevention messages to these communities. Integrating these needs into existing Australian health policy and practice is of paramount importance for reducing obesity-related disparities currently prevailing in Australia. What is known about the topic? Childhood obesity prevalence is plateauing in developed countries including Australia; however, obesity-related inequalities continue to exist in Australia especially among communities living in disadvantaged areas, which experience poor engagement in childhood obesity prevention initiatives. Studies in the USA have found that assessing disadvantaged communities' readiness to participate in health programs is a critical initial step in reducing the disproportionate obesity burden among these communities. However, no studies in Australia have assessed disadvantaged communities' readiness to engage in obesity prevention initiatives. What does this paper add? This paper addresses the current gap in the knowledge of disadvantaged communities' level of readiness to engage in childhood obesity prevention initiatives in Australia. The study also identified the key factors responsible for low readiness of disadvantaged communities to participate in current childhood obesity prevention services. By using the Community Readiness model this study shows the readiness levels specific to the various dimensions of the model; Understanding dimension-specific readiness allows us to identify strategies that are tailored to each dimension, as guided by the model. What are the implications for practitioners? With the increasing burden of childhood obesity on disadvantaged communities, policymakers and health practitioners are facing a crisis in obesity prevention and management. Almost every year, new interventions are being planned and implemented. However if the target communities are not ready to participate in the available interventions these efforts are futile. This study exposes the key factors responsible for low readiness to participate in current obesity prevention services by disadvantaged communities. Addressing these key factors and improving readiness before designing new interventions will improve the participation of disadvantaged communities in those interventions. The study findings ultimately have the potential of reducing obesity-related disparities in Australia.

What Are the Costs of Trauma Center Readiness? Defining and Standardizing Readiness Costs for Trauma Centers Statewide.

PubMed

Ashley, Dennis W; Mullins, Robert F; Dente, Christopher J; Garlow, Laura; Medeiros, Regina S; Atkins, Elizabeth V; Solomon, Gina; Abston, Dena; Ferdinand, Colville H

2017-09-01

Trauma center readiness costs are incurred to maintain essential infrastructure and capacity to provide emergent services on a 24/7 basis. These costs are not captured by traditional hospital cost accounting, and no national consensus exists on appropriate definitions for each cost. Therefore, in 2010, stakeholders from all Level I and II trauma centers developed a survey tool standardizing and defining trauma center readiness costs. The survey tool underwent minor revisions to provide further clarity, and the survey was repeated in 2013. The purpose of this study was to provide a follow-up analysis of readiness costs for Georgia's Level I and Level II trauma centers. Using the American College of Surgeons Resources for Optimal Care of the Injured Patient guidelines, four readiness cost categories were identified: Administrative, Clinical Medical Staff, Operating Room, and Education/Outreach. Through conference calls, webinars and face-to-face meetings with financial officers, trauma medical directors, and program managers from all trauma centers, standardized definitions for reporting readiness costs within each category were developed. This resulted in a survey tool for centers to report their individual readiness costs for one year. The total readiness cost for all Level I trauma centers was $34,105,318 (avg $6,821,064) and all Level II trauma centers was $20,998,019 (avg $2,333,113). Methodology to standardize and define readiness costs for all trauma centers within the state was developed. Average costs for Level I and Level II trauma centers were identified. This model may be used to help other states define and standardize their trauma readiness costs.

StormReady in a Box: Enhancing NOAA's Presence in Schools

NASA Astrophysics Data System (ADS)

Grondin, N. S.; Franks, C.

2015-12-01

The National Weather Service StormReady Supporter program exists to give schools, companies, TV stations, and other facilities the opportunity to earn recognition for their weather preparedness and awareness. Requirements to earn StormReady Supporter status include having a facility warning point, use of NOAA Weather Radios, and weather hazard Emergency Operation Plans. Despite the increasing importance of weather preparedness in schools, only 1.2% of Minnesota schools are deemed StormReady by the National Weather Service. It was determined that the major impedance for schools becoming StormReady Supporters is the lack of time for administrators to engage in anything "extra" beyond their listed duties. As part of a 2015 Hollings Scholar project, the StormReady in a Box concept was developed to remedy this, by empowering teachers and students to take charge and complete the StormReady Supporter application for their school. StormReady in a Box is a project developed for Junior High School students to learn about weather preparedness and to help their school acquire StormReady status. The project was designed to be relevant to the Minnesota State Education Standards in Science, be simple for teachers to do with their students, and most importantly, to be enjoyable for Junior High School age students to do. The project was also designed to enhance critical thinking skills and logical reasoning abilities, as they relate to the StormReady Supporter application. This presentation will present the overall rationale for the undertaking of this project, the creation of, and the logical next steps for the StormReady in a Box project.

Characterization of genomic sequence showing strong association with polyembryony among diverse Citrus species and cultivars, and its synteny with Vitis and Populus.

PubMed

Nakano, Michiharu; Shimada, Takehiko; Endo, Tomoko; Fujii, Hiroshi; Nesumi, Hirohisa; Kita, Masayuki; Ebina, Masumi; Shimizu, Tokurou; Omura, Mitsuo

2012-02-01

Polyembryony, in which multiple somatic nucellar cell-derived embryos develop in addition to the zygotic embryo in a seed, is common in the genus Citrus. Previous genetic studies indicated polyembryony is mainly determined by a single locus, but the underlying molecular mechanism is still unclear. As a step towards identification and characterization of the gene or genes responsible for nucellar embryogenesis in Citrus, haplotype-specific physical maps around the polyembryony locus were constructed. By sequencing three BAC clones aligned on the polyembryony haplotype, a single contiguous draft sequence consisting of 380 kb containing 70 predicted open reading frames (ORFs) was reconstructed. Single nucleotide polymorphism genotypes detected in the sequenced genomic region showed strong association with embryo type in Citrus, indicating a common polyembryony locus is shared among widely diverse Citrus cultivars and species. The arrangement of the predicted ORFs in the characterized genomic region showed high collinearity to the genomic sequence of chromosome 4 of Vitis vinifera and linkage group VI of Populus trichocarpa, suggesting that the syntenic relationship among these species is conserved even though V. vinifera and P. trichocarpa are non-apomictic species. This is the first study to characterize in detail the genomic structure of an apomixis locus determining adventitious embryony. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Identification and characterization of Highlands J virus from a Mississippi sandhill crane using unbiased next-generation sequencing

USGS Publications Warehouse

Ip, Hon S.; Wiley, Michael R.; Long, Renee; Gustavo, Palacios; Shearn-Bochsler, Valerie; Whitehouse, Chris A.

2014-01-01

Advances in massively parallel DNA sequencing platforms, commonly termed next-generation sequencing (NGS) technologies, have greatly reduced time, labor, and cost associated with DNA sequencing. Thus, NGS has become a routine tool for new viral pathogen discovery and will likely become the standard for routine laboratory diagnostics of infectious diseases in the near future. This study demonstrated the application of NGS for the rapid identification and characterization of a virus isolated from the brain of an endangered Mississippi sandhill crane. This bird was part of a population restoration effort and was found in an emaciated state several days after Hurricane Isaac passed over the refuge in Mississippi in 2012. Post-mortem examination had identified trichostrongyliasis as the possible cause of death, but because a virus with morphology consistent with a togavirus was isolated from the brain of the bird, an arboviral etiology was strongly suspected. Because individual molecular assays for several known arboviruses were negative, unbiased NGS by Illumina MiSeq was used to definitively identify and characterize the causative viral agent. Whole genome sequencing and phylogenetic analysis revealed the viral isolate to be the Highlands J virus, a known avian pathogen. This study demonstrates the use of unbiased NGS for the rapid detection and characterization of an unidentified viral pathogen and the application of this technology to wildlife disease diagnostics and conservation medicine.

Improving Correlation Algorithms to Detect and Characterize Smaller Magnitude Induced Seismicity Swarms

NASA Astrophysics Data System (ADS)

Skoumal, R.; Brudzinski, M.; Currie, B.

2015-12-01

Induced seismic sequences often occur as swarms that can include thousands of small (< M 2) earthquakes. While the identification of this microseismicity would invariably aid in the characterization and modeling of induced sequences, traditional earthquake detection techniques often provide incomplete catalogs, even when local networks are deployed. Because induced sequences often include scores of micro-earthquakes that prelude larger magnitude events, the identification of these small magnitude events would be crucial for the early identification of induced sequences. By taking advantage of the repeating, swarm-like nature of induced seismicity, a more robust catalog can be created using complementary correlation algorithms in near real-time without the reliance on traditional earthquake detection and association routines. Since traditional earthquake catalog methodologies using regional networks have a relatively high detection threshold (M 2+), we have sought to develop correlation routines that can detect smaller magnitude sequences. While short-term/long-term amplitude average detection algorithms requires significant signal-to-noise ratio at multiple stations for confident identification, a correlation detector is capable of identifying earthquakes with high confidence using just a single station. The result is an embarrassingly parallel task that can be employed for a network to be used as an early warning system for potentially induced seismicity while also better characterizing tectonic sequences beyond what traditional methods allow.

SVS: data and knowledge integration in computational biology.

PubMed

Zycinski, Grzegorz; Barla, Annalisa; Verri, Alessandro

2011-01-01

In this paper we present a framework for structured variable selection (SVS). The main concept of the proposed schema is to take a step towards the integration of two different aspects of data mining: database and machine learning perspective. The framework is flexible enough to use not only microarray data, but other high-throughput data of choice (e.g. from mass spectrometry, microarray, next generation sequencing). Moreover, the feature selection phase incorporates prior biological knowledge in a modular way from various repositories and is ready to host different statistical learning techniques. We present a proof of concept of SVS, illustrating some implementation details and describing current results on high-throughput microarray data.

Recombinational Cloning Using Gateway and In-Fusion Cloning Schemes

PubMed Central

Throop, Andrea L.; LaBaer, Joshua

2015-01-01

The comprehensive study of protein structure and function, or proteomics, depends on the obtainability of full-length cDNAs in species-specific expression vectors and subsequent functional analysis of the expressed protein. Recombinational cloning is a universal cloning technique based on site-specific recombination that is independent of the insert DNA sequence of interest, which differentiates this method from the classical restriction enzyme-based cloning methods. Recombinational cloning enables rapid and efficient parallel transfer of DNA inserts into multiple expression systems. This unit summarizes strategies for generating expression-ready clones using the most popular recombinational cloning technologies, including the commercially available Gateway® (Life Technologies) and In-Fusion® (Clontech) cloning technologies. PMID:25827088

A Planetarium Inside Your Office: Virtual Reality in the Dome Production Pipeline

NASA Astrophysics Data System (ADS)

Summers, Frank

2018-01-01

Producing astronomy visualization sequences for a planetarium without ready access to a dome is a distorted geometric challenge. Fortunately, one can now use virtual reality (VR) to simulate a dome environment without ever leaving one's office chair. The VR dome experience has proven to be a more than suitable pre-visualization method that requires only modest amounts of processing beyond the standard production pipeline. It also provides a crucial testbed for identifying, testing, and fixing the visual constraints and artifacts that arise in a spherical presentation environment. Topics adreesed here will include rendering, geometric projection, movie encoding, software playback, and hardware setup for a virtual dome using VR headsets.

TRL-6 for JWST wavefront sensing and control

NASA Astrophysics Data System (ADS)

Feinberg, Lee D.; Dean, Bruce H.; Aronstein, David L.; Bowers, Charles W.; Hayden, William; Lyon, Richard G.; Shiri, Ron; Smith, J. Scott; Acton, D. Scott; Carey, Larkin; Contos, Adam; Sabatke, Erin; Schwenker, John; Shields, Duncan; Towell, Tim; Shi, Fang; Meza, Luis

2007-09-01

NASA's Technology Readiness Level (TRL)-6 is documented for the James Webb Space Telescope (JWST) Wavefront Sensing and Control (WFSC) subsystem. The WFSC subsystem is needed to align the Optical Telescope Element (OTE) after all deployments have occurred, and achieves that requirement through a robust commissioning sequence consisting of unique commissioning algorithms, all of which are part of the WFSC algorithm suite. This paper identifies the technology need, algorithm heritage, describes the finished TRL-6 design platform, and summarizes the TRL-6 test results and compliance. Additionally, the performance requirements needed to satisfy JWST science goals as well as the criterion that relate to the TRL-6 Testbed Telescope (TBT) performance requirements are discussed.

TRL-6 for JWST Wavefront Sensing and Control

NASA Technical Reports Server (NTRS)

Feinberg, Lee; Dean, Bruce; Smith, Scott; Aronstein, David; Shiri, Ron; Lyon, Rick; Hayden, Bill; Bowers, Chuck; Acton, D. Scott; Shields, Duncan;

The Deep Space Network

NASA Technical Reports Server (NTRS)

1975-01-01

The primary objectives during this portion of the extended mission were to assure survival of the spacecraft for a third Mercury encounter through conservation of attitude control gas and to conduct trajectory correction maneuvers (TCMs) as necessary to target the spacecraft for a solar occultation zone pass. Special support activities included TCMs 6 and 7 conducted on October 30, 1974 and on February 12-13, 1975, respectively. This period also saw the DSN interface organization involved in (1) the allocation of sufficient coverage to assure accurate orbit determination solutions, (2) monitoring of DSN implementation for Viking to assure maintenance of compatible interfaces and capabilities required for Mariner 10, and (3) the development of encounter coverage, sequences, and readiness test plans.

The Condition of College & Career Readiness 2016: Oregon Key Findings

ERIC Educational Resources Information Center

ACT, Inc., 2016

2016-01-01

"The Condition of College and Career Readiness" looks at the progress of the 2016 ACT®-tested graduating class relative to college and career readiness. This state briefing begins with statistics in the following categories for Oregon: performance, STEM, career readiness, impact, behaviors that impact access and opportunity, pipeline,…

The Condition of College & Career Readiness 2016: Minnesota Key Findings

ERIC Educational Resources Information Center

ACT, Inc., 2016

2016-01-01

"The Condition of College and Career Readiness" looks at the progress of the 2016 ACT®-tested graduating class relative to college and career readiness. This state briefing begins with statistics in the following categories for Minnesota: performance, STEM, career readiness, impact, behaviors that impact access and opportunity, pipeline,…

The Condition of College & Career Readiness 2016: Virginia Key Findings

ERIC Educational Resources Information Center

ACT, Inc., 2016

2016-01-01

"The Condition of College and Career Readiness" looks at the progress of the 2016 ACT®-tested graduating class relative to college and career readiness. This state briefing begins with statistics in the following categories for Virginia: performance, STEM, career readiness, impact, behaviors that impact access and opportunity, pipeline,…

Neuroscience Perspectives on Disparities in School Readiness and Cognitive Achievement

ERIC Educational Resources Information Center

Noble, Kimberly G.; Tottenham, Nim; Casey, B. J.

2005-01-01

This article allows readers to look at racial and ethnic disparities in school readiness from a neuroscience perspective. Although researchers have traditionally measured gaps in school readiness using broad achievement tests, they can now assess readiness in terms of more specific brain-based cognitive functions. Three neurocognitive…

State College and Career Readiness Initiative: Statewide Transitional Courses for College Readiness

ERIC Educational Resources Information Center

Barger, Kenna; Murray, Renee; Smith, Janie

2011-01-01

Through the "Strengthening Statewide College/Career Readiness Initiative" (SSCRI), Southern Regional Education Board (SREB) has collaborated with states on state policy goals and actions needed to improve high school students' academic readiness for postsecondary study and reduce the need for remedial work. SREB created and implemented…

The Condition of College & Career Readiness 2016: Pennsylvania Key Findings

ERIC Educational Resources Information Center

ACT, Inc., 2016

2016-01-01

"The Condition of College and Career Readiness" looks at the progress of the 2016 ACT®-tested graduating class relative to college and career readiness. This state briefing begins with statistics in the following categories for Pennsylvania: performance, STEM, career readiness, impact, behaviors that impact access and opportunity,…

The Reality of College Readiness, 2012. North Carolina

ERIC Educational Resources Information Center

ACT, Inc., 2012

2012-01-01

Annually, ACT provides each state with "The Condition of College & Career Readiness," a report that details the college readiness of students who took the ACT[R] test. This report is a companion to "The Condition of College & Career Readiness." This paper traces the college enrollment, retention, re-enrollment, and…

The Reality of College Readiness, 2012. South Carolina

ERIC Educational Resources Information Center

ACT, Inc., 2012

2012-01-01

Annually, ACT provides each state with "The Condition of College & Career Readiness," a report that details the college readiness of students who took the ACT[R] test. This report is a companion to "The Condition of College & Career Readiness." This paper traces the college enrollment, retention, re-enrollment, and…

The Career Readiness Certificate: The Foundation for Stackable Credentials

ERIC Educational Resources Information Center

Bolin, Barbara

2011-01-01

This article features the Career Readiness Certificate (CRC) which serves as the founding credential in the six states and one locality in the Career Readiness Certificate Consortium (Tennessee, West Virginia, Kentucky, Maryland, North Carolina, Virginia and Washington, D.C.). The Career Readiness Certificate was developed by the small consortium…

The Condition of College & Career Readiness 2016: Michigan Key Findings

ERIC Educational Resources Information Center

ACT, Inc., 2016

2016-01-01

"The Condition of College and Career Readiness" looks at the progress of the 2016 ACT®-tested graduating class relative to college and career readiness. This state briefing begins with statistics in the following categories for Michigan: performance, STEM, career readiness, impact, behaviors that impact access and opportunity, pipeline,…

Validation of the Lollipop Test: A Diagnostic Screening Test of School Readiness.

ERIC Educational Resources Information Center

Chew, Alex L.; Morris, John D.

1984-01-01

The validity of the Lollipop Test: A Diagnostic Screening Test of School Readiness was examined using the Metropolitan Readiness Test (MRT), Level I, Form Q, as the criterion. Appreciable concurrent validity was found across test batteries. Implications for school readiness screening are discussed. (Author/BS)

The Condition of College & Career Readiness 2016: Idaho Key Findings

ERIC Educational Resources Information Center

ACT, Inc., 2016

2016-01-01

"The Condition of College and Career Readiness" looks at the progress of the 2016 ACT®-tested graduating class relative to college and career readiness. This state briefing begins with statistics in the following categories for Idaho: performance, STEM, career readiness, impact, behaviors that impact access and opportunity, pipeline, and…

The Reality of College Readiness, 2012. New Hampshire

ERIC Educational Resources Information Center

ACT, Inc., 2012

2012-01-01

Annually, ACT provides each state with "The Condition of College & Career Readiness," a report that details the college readiness of students who took the ACT[R] test. This report is a companion to "The Condition of College & Career Readiness." This paper traces the college enrollment, retention, re-enrollment, and…

The Condition of College & Career Readiness 2016: Hawaii Key Findings

ERIC Educational Resources Information Center

ACT, Inc., 2016

2016-01-01

"The Condition of College and Career Readiness" looks at the progress of the 2016 ACT®-tested graduating class relative to college and career readiness. This state briefing begins with statistics in the following categories for Hawaii: performance, STEM, career readiness, impact, behaviors that impact access and opportunity, pipeline,…

Readiness Matters! 2014-2015 Kindergarten Readiness Assessment

ERIC Educational Resources Information Center

Maryland State Department of Education, 2015

2015-01-01

Maryland's demanding new Kindergarten Readiness Assessment was administered statewide for the first time. Its results are revealing and sobering. Many states do not even check in any systematic way on their children's readiness for kindergarten, and in previous years, Maryland used metrics based on modest expectations, outdated standards, and…

The Condition of College & Career Readiness, 2010

ERIC Educational Resources Information Center

ACT, Inc., 2010

2010-01-01

Since 1959, ACT has collected and reported data on students' academic readiness for college. Because becoming ready for college and career is a process that occurs throughout elementary and secondary education, measuring academic performance over time in the context of college and career readiness provides meaningful and compelling information…

What Are the ACT College Readiness Benchmarks? Information Brief

ERIC Educational Resources Information Center

ACT, Inc., 2013

2013-01-01

The ACT College Readiness Benchmarks are the minimum ACT® college readiness assessment scores required for students to have a high probability of success in credit-bearing college courses--English Composition, social sciences courses, College Algebra, or Biology. This report identifies the College Readiness Benchmarks on the ACT Compass scale…

The Condition of College & Career Readiness 2016: Wisconsin Key Findings

ERIC Educational Resources Information Center

ACT, Inc., 2016

2016-01-01

"The Condition of College and Career Readiness" looks at the progress of the 2016 ACT®-tested graduating class relative to college and career readiness. This state briefing begins with statistics in the following categories for Wisconsin: performance, STEM, career readiness, impact, behaviors that impact access and opportunity, pipeline,…

Determining transition readiness in congenital heart disease: Assessing the utility of the Transition Readiness Questionnaire

USDA-ARS?s Scientific Manuscript database

The Transition Readiness Assessment Questionnaire (TRAQ) is a tool commonly used to assess transition readiness in adolescents with chronic diseases. It was previously validated in youth with special health care needs (YSHCN), but no patients with congenital heart disease (CHD) were included in the ...

Understanding Readiness: An Occasional Paper.

ERIC Educational Resources Information Center

Jensen, Arthur R.

Readiness to learn occurs when a child has achieved cumulative learning of component subskills and the developmental maturity necessary to integrate these subskills into the desired skill. Readiness is relative, however, not only to the skill, but also to the technique of instruction. Thus, readiness for learning a particular skill by different…

Characterization of NIST human mitochondrial DNA SRM-2392 and SRM-2392-I standard reference materials by next generation sequencing.

PubMed

Riman, Sarah; Kiesler, Kevin M; Borsuk, Lisa A; Vallone, Peter M

2017-07-01

Standard Reference Materials SRM 2392 and 2392-I are intended to provide quality control when amplifying and sequencing human mitochondrial genome sequences. The National Institute of Standards and Technology (NIST) offers these SRMs to laboratories performing DNA-based forensic human identification, molecular diagnosis of mitochondrial diseases, mutation detection, evolutionary anthropology, and genetic genealogy. The entire mtGenome (∼16569bp) of SRM 2392 and 2392-I have previously been characterized at NIST by Sanger sequencing. Herein, we used the sensitivity, specificity, and accuracy offered by next generation sequencing (NGS) to: (1) re-sequence the certified values of the SRM 2392 and 2392-I; (2) confirm Sanger data with a high coverage new sequencing technology; (3) detect lower level heteroplasmies (<20%); and thus (4) support mitochondrial sequencing communities in the adoption of NGS methods. To obtain a consensus sequence for the SRMs as well as identify and control any bias, sequencing was performed using two NGS platforms and data was analyzed using different bioinformatics pipelines. Our results confirm five low level heteroplasmy sites that were not previously observed with Sanger sequencing: three sites in the GM09947A template in SRM 2392 and two sites in the HL-60 template in SRM 2392-I. Copyright © 2017 Elsevier B.V. All rights reserved.

Characterization of the complete chloroplast genome of Platycarya strobilacea (Juglandaceae)

Treesearch

Jing Yan; Kai Han; Shuyun Zeng; Peng Zhao; Keith Woeste; Jianfang Li; Zhan-Lin Liu

2017-01-01

The whole chloroplast genome (cp genome) sequence of Platycarya strobilacea was characterized from Illumina pair-end sequencing data. The complete cp genome was 160,994 bp in length and contained a large single copy region (LSC) of 90,225 bp and a small single copy region (SSC) of 18,371 bp, which were separated by a pair of inverted repeat regions...

Complete genome sequence of Campylobacter concisus ATCC 33237T and draft genome sequences for an additional eight well-characterized C. concisus strains

USDA-ARS?s Scientific Manuscript database

This report includes the complete genome of the Campylobacter concisus type strain ATCC 33237T and the draft genomes of eight additional well characterized C. concisus genomes. C. concisus has been shown to be a genetically heterogeneous species and these nine genomes provide valuable information re...

Comparative genome analysis and characterization of the Salmonella Typhimurium strain CCRJ_26 isolated from swine carcasses using whole-genome sequencing approach.

PubMed

Panzenhagen, P H N; Cabral, C C; Suffys, P N; Franco, R M; Rodrigues, D P; Conte-Junior, C A

2018-04-01

Salmonella pathogenicity relies on virulence factors many of which are clustered within the Salmonella pathogenicity islands. Salmonella also harbours mobile genetic elements such as virulence plasmids, prophage-like elements and antimicrobial resistance genes which can contribute to increase its pathogenicity. Here, we have genetically characterized a selected S. Typhimurium strain (CCRJ_26) from our previous study with Multiple Drugs Resistant profile and high-frequency PFGE clonal profile which apparently persists in the pork production centre of Rio de Janeiro State, Brazil. By whole-genome sequencing, we described the strain's genome virulent content and characterized the repertoire of bacterial plasmids, antibiotic resistance genes and prophage-like elements. Here, we have shown evidence that strain CCRJ_26 genome possible represent a virulence-associated phenotype which may be potentially virulent in human infection. Whole-genome sequencing technologies are still costly and remain underexplored for applied microbiology in Brazil. Hence, this genomic description of S. Typhimurium strain CCRJ_26 will provide help in future molecular epidemiological studies. The analysis described here reveals a quick and useful pipeline for bacterial virulence characterization using whole-genome sequencing approach. © 2018 The Society for Applied Microbiology.

TaxI: a software tool for DNA barcoding using distance methods

PubMed Central

Steinke, Dirk; Vences, Miguel; Salzburger, Walter; Meyer, Axel

2005-01-01

DNA barcoding is a promising approach to the diagnosis of biological diversity in which DNA sequences serve as the primary key for information retrieval. Most existing software for evolutionary analysis of DNA sequences was designed for phylogenetic analyses and, hence, those algorithms do not offer appropriate solutions for the rapid, but precise analyses needed for DNA barcoding, and are also unable to process the often large comparative datasets. We developed a flexible software tool for DNA taxonomy, named TaxI. This program calculates sequence divergences between a query sequence (taxon to be barcoded) and each sequence of a dataset of reference sequences defined by the user. Because the analysis is based on separate pairwise alignments this software is also able to work with sequences characterized by multiple insertions and deletions that are difficult to align in large sequence sets (i.e. thousands of sequences) by multiple alignment algorithms because of computational restrictions. Here, we demonstrate the utility of this approach with two datasets of fish larvae and juveniles from Lake Constance and juvenile land snails under different models of sequence evolution. Sets of ribosomal 16S rRNA sequences, characterized by multiple indels, performed as good as or better than cox1 sequence sets in assigning sequences to species, demonstrating the suitability of rRNA genes for DNA barcoding. PMID:16214755

Sequence stratigraphic controls on reservoir characterization and architecture: case study of the Messinian Abu Madi incised-valley fill, Egypt

NASA Astrophysics Data System (ADS)

Abdel-Fattah, Mohamed I.; Slatt, Roger M.

2013-12-01

Understanding sequence stratigraphy architecture in the incised-valley is a crucial step to understanding the effect of relative sea level changes on reservoir characterization and architecture. This paper presents a sequence stratigraphic framework of the incised-valley strata within the late Messinian Abu Madi Formation based on seismic and borehole data. Analysis of sand-body distribution reveals that fluvial channel sandstones in the Abu Madi Formation in the Baltim Fields, offshore Nile Delta, Egypt, are not randomly distributed but are predictable in their spatial and stratigraphic position. Elucidation of the distribution of sandstones in the Abu Madi incised-valley fill within a sequence stratigraphic framework allows a better understanding of their characterization and architecture during burial. Strata of the Abu Madi Formation are interpreted to comprise two sequences, which are the most complex stratigraphically; their deposits comprise a complex incised valley fill. The lower sequence (SQ1) consists of a thick incised valley-fill of a Lowstand Systems Tract (LST1)) overlain by a Transgressive Systems Tract (TST1) and Highstand Systems Tract (HST1). The upper sequence (SQ2) contains channel-fill and is interpreted as a LST2 which has a thin sandstone channel deposits. Above this, channel-fill sandstone and related strata with tidal influence delineates the base of TST2, which is overlain by a HST2. Gas reservoirs of the Abu Madi Formation (present-day depth ˜3552 m), the Baltim Fields, Egypt, consist of fluvial lowstand systems tract (LST) sandstones deposited in an incised valley. LST sandstones have a wide range of porosity (15 to 28%) and permeability (1 to 5080mD), which reflect both depositional facies and diagenetic controls. This work demonstrates the value of constraining and evaluating the impact of sequence stratigraphic distribution on reservoir characterization and architecture in incised-valley deposits, and thus has an important impact on reservoir quality evolution in hydrocarbon exploration in such settings.

Cloning and characterization of the gene encoding IMP dehydrogenase from Arabidopsis thaliana.

PubMed

Collart, F R; Osipiuk, J; Trent, J; Olsen, G J; Huberman, E

1996-10-03

We have cloned and characterized the gene encoding inosine monophosphate dehydrogenase (IMPDH) from Arabidopsis thaliana (At). The transcription unit of the At gene spans approximately 1900 bp and specifies a protein of 503 amino acids with a calculated relative molecular mass (M(r)) of 54,190. The gene is comprised of a minimum of four introns and five exons with all donor and acceptor splice sequences conforming to previously proposed consensus sequences. The deduced IMPDH amino-acid sequence from At shows a remarkable similarity to other eukaryotic IMPDH sequences, with a 48% identity to human Type II enzyme. Allowing for conservative substitutions, the enzyme is 69% similar to human Type II IMPDH. The putative active-site sequence of At IMPDH conforms to the IMP dehydrogenase/guanosine monophosphate reductase motif and contains an essential active-site cysteine residue.

Extensive characterization of Tupaia belangeri neuropeptidome using an integrated mass spectrometric approach.

PubMed

Petruzziello, Filomena; Fouillen, Laetitia; Wadensten, Henrik; Kretz, Robert; Andren, Per E; Rainer, Gregor; Zhang, Xiaozhe

2012-02-03

Neuropeptidomics is used to characterize endogenous peptides in the brain of tree shrews (Tupaia belangeri). Tree shrews are small animals similar to rodents in size but close relatives of primates, and are excellent models for brain research. Currently, tree shrews have no complete proteome information available on which direct database search can be allowed for neuropeptide identification. To increase the capability in the identification of neuropeptides in tree shrews, we developed an integrated mass spectrometry (MS)-based approach that combines methods including data-dependent, directed, and targeted liquid chromatography (LC)-Fourier transform (FT)-tandem MS (MS/MS) analysis, database construction, de novo sequencing, precursor protein search, and homology analysis. Using this integrated approach, we identified 107 endogenous peptides that have sequences identical or similar to those from other mammalian species. High accuracy MS and tandem MS information, with BLAST analysis and chromatographic characteristics were used to confirm the sequences of all the identified peptides. Interestingly, further sequence homology analysis demonstrated that tree shrew peptides have a significantly higher degree of homology to equivalent sequences in humans than those in mice or rats, consistent with the close phylogenetic relationship between tree shrews and primates. Our results provide the first extensive characterization of the peptidome in tree shrews, which now permits characterization of their function in nervous and endocrine system. As the approach developed fully used the conservative properties of neuropeptides in evolution and the advantage of high accuracy MS, it can be portable for identification of neuropeptides in other species for which the fully sequenced genomes or proteomes are not available.

Characterization of an endogenous retrovirus class in elephants and their relatives

PubMed Central

Greenwood, Alex D; Englbrecht, Claudia C; MacPhee, Ross DE

2004-01-01

Background Endogenous retrovirus-like elements (ERV-Ls, primed with tRNA leucine) are a diverse group of reiterated sequences related to foamy viruses and widely distributed among mammals. As shown in previous investigations, in many primates and rodents this class of elements has remained transpositionally active, as reflected by increased copy number and high sequence diversity within and among taxa. Results Here we examine whether proviral-like sequences may be suitable molecular probes for investigating the phylogeny of groups known to have high element diversity. As a test we characterized ERV-Ls occurring in a sample of extant members of superorder Uranotheria (Asian and African elephants, manatees, and hyraxes). The ERV-L complement in this group is even more diverse than previously suspected, and there is sequence evidence for active expansion, particularly in elephantids. Many of the elements characterized have protein coding potential suggestive of activity. Conclusions In general, the evidence supports the hypothesis that the complement had a single origin within basal Uranotheria. PMID:15476555

Mining and gene ontology based annotation of SSR markers from expressed sequence tags of Humulus lupulus

PubMed Central

Singh, Swati; Gupta, Sanchita; Mani, Ashutosh; Chaturvedi, Anoop

2012-01-01

Humulus lupulus is commonly known as hops, a member of the family moraceae. Currently many projects are underway leading to the accumulation of voluminous genomic and expressed sequence tag sequences in public databases. The genetically characterized domains in these databases are limited due to non-availability of reliable molecular markers. The large data of EST sequences are available in hops. The simple sequence repeat markers extracted from EST data are used as molecular markers for genetic characterization, in the present study. 25,495 EST sequences were examined and assembled to get full-length sequences. Maximum frequency distribution was shown by mononucleotide SSR motifs i.e. 60.44% in contig and 62.16% in singleton where as minimum frequency are observed for hexanucleotide SSR in contig (0.09%) and pentanucleotide SSR in singletons (0.12%). Maximum trinucleotide motifs code for Glutamic acid (GAA) while AT/TA were the most frequent repeat of dinucleotide SSRs. Flanking primer pairs were designed in-silico for the SSR containing sequences. Functional categorization of SSRs containing sequences was done through gene ontology terms like biological process, cellular component and molecular function. PMID:22368382

De novo characterization of Lentinula edodes C(91-3) transcriptome by deep Solexa sequencing.

PubMed

Zhong, Mintao; Liu, Ben; Wang, Xiaoli; Liu, Lei; Lun, Yongzhi; Li, Xingyun; Ning, Anhong; Cao, Jing; Huang, Min

2013-02-01

Lentinula edodes, has been utilized as food, as well as, in popular medicine, moreover, its extract isolated from its mycelium and fruiting body have shown several therapeutic properties. Yet little is understood about its genes involved in these properties, and the absence of L.edodes genomes has been a barrier to the development of functional genomics research. However, high throughput sequencing technologies are now being widely applied to non-model species. To facilitate research on L.edodes, we leveraged Solexa sequencing technology in de novo assembly of L.edodes C(91-3) transcriptome. In a single run, we produced more than 57 million sequencing reads. These reads were assembled into 28,923 unigene sequences (mean size=689bp) including 18,120 unigenes with coding sequence (CDS). Based on similarity search with known proteins, assembled unigene sequences were annotated with gene descriptions, gene ontology (GO) and clusters of orthologous group (COG) terms. Our data provides the first comprehensive sequence resource available for functional genomics studies in L.edodes, and demonstrates the utility of Illumina/Solexa sequencing for de novo transcriptome characterization and gene discovery in a non-model mushroom. Copyright © 2012 Elsevier Inc. All rights reserved.

Quantiprot - a Python package for quantitative analysis of protein sequences.

PubMed

Konopka, Bogumił M; Marciniak, Marta; Dyrka, Witold

2017-07-17

The field of protein sequence analysis is dominated by tools rooted in substitution matrices and alignments. A complementary approach is provided by methods of quantitative characterization. A major advantage of the approach is that quantitative properties defines a multidimensional solution space, where sequences can be related to each other and differences can be meaningfully interpreted. Quantiprot is a software package in Python, which provides a simple and consistent interface to multiple methods for quantitative characterization of protein sequences. The package can be used to calculate dozens of characteristics directly from sequences or using physico-chemical properties of amino acids. Besides basic measures, Quantiprot performs quantitative analysis of recurrence and determinism in the sequence, calculates distribution of n-grams and computes the Zipf's law coefficient. We propose three main fields of application of the Quantiprot package. First, quantitative characteristics can be used in alignment-free similarity searches, and in clustering of large and/or divergent sequence sets. Second, a feature space defined by quantitative properties can be used in comparative studies of protein families and organisms. Third, the feature space can be used for evaluating generative models, where large number of sequences generated by the model can be compared to actually observed sequences.

Contribution entrepreneurial knowledge, skills competence, and self-efficacy to student entrepreneurship readiness of multimedia expertise at vocational high school in Malang

NASA Astrophysics Data System (ADS)

Islami, Pio Arfianova Ftirizky; Elmunsyah, Hakkun; Muladi

2017-09-01

This study aims to determine the contribution of entrepreneurship knowledge, skills competence, and self-efficacy to entrepreneurship readiness. The design used in this research using a quantitative approach and knowledge test techniques using regression analysis. The number of samples in this study as many as 181 students. The results showed that there was a significant contribution between entrepreneurship knowledge to entrepreneurship readiness. There is also a significant contribution between the skills competence to entrepreneurship readiness and there is a significant contribution between self-efficacy to entrepreneurship readiness. Futhermore, there is a significant contribution simultaneously between entrepreneurship knowledge, skill competence; self-efficacy to entrepreneurship readiness.

Genetic Characterization of Listeria monocytogenes Isolates from Industrial and Retail Ready-to-Eat Meat-Based Foods and Their Relationship with Clinical Strains from Human Listeriosis in Portugal.

PubMed

Henriques, A R; Cristino, J Melo; Fraqueza, M J

2017-04-01

Listeria monocytogenes isolates (n = 81) recovered from ready-to-eat meat-based food products (RTEMP) collected in industrial processing plants and retail establishments were genetically characterized for comparison with those from human clinical cases of listeriosis (n = 49). The aim was to assess RTEMP as a possible food source for human infection. L. monocytogenes was detected in 12.5% of the RTEMP samples, and in some cases, counts were above the European food safety criteria. All isolates were assessed by multiplex PCR for serogroup determination and detection of virulence-associated genes inlA, inlB, inlC, inlJ, plcA, hlyA, actA, and iap. Serogroups IIb and IVb dominated in RTEMP and human isolates, and all were positive for the assessed virulence genes. Antibiotic susceptibility testing by the disk diffusion method revealed a low level of resistance among the isolates. Pulsed-field gel electrophoresis (PFGE) of L. monocytogenes isolates, using restriction enzymes ApaI and AscI, revealed genetic variability and differentiated the isolates in five clusters. Although some pulsed-field gel electrophoresis profiles of particular RTEMP and human isolates seemed to be highly related, exhibiting more than 90% similarity, which suggests a possible common source, in most cases the strains were not genetically or temporally matched. The close genetic relatedness of RTEMP and human listeriosis strains stressed the importance of preventive measure implementation throughout the food chain.

A proteomic study to identify soya allergens--the human response to transgenic versus non-transgenic soya samples.

PubMed

Batista, Rita; Martins, Isabel; Jeno, Paul; Ricardo, Cândido Pinto; Oliveira, Maria Margarida

2007-01-01

In spite of being among the main foods responsible for allergic reactions worldwide, soybean (Glycine max)-derived products continue to be increasingly widespread in a variety of food products due to their well-documented health benefits. Soybean also continues to be one of the elected target crops for genetic modification. The aim of this study was to characterize the soya proteome and, specifically, IgE-reactive proteins as well as to compare the IgE response in soya-allergic individuals to genetically modified Roundup Ready soya versus its non-transgenic control. We performed two-dimensional gel electrophoresis of protein extracts from a 5% genetically modified Roundup Ready flour sample and its non-transgenic control followed by Western blotting with plasma from 5 soya-sensitive individuals. We used peptide tandem mass spectrometry to identify soya proteins (55 protein matches), specifically IgE-binding ones, and to evaluate differences between transgenic and non-transgenic samples. We identified 2 new potential soybean allergens--one is maturation associated and seems to be part of the late embryogenesis abundant proteins group and the other is a cysteine proteinase inhibitor. None of the individuals tested reacted differentially to the transgenic versus non-transgenic samples under study. Soybean endogenous allergen expression does not seem to be altered after genetic modification. Proteomics should be considered a powerful tool for functional characterization of plants and for food safety assessment. Copyright (c) 2007 S. Karger AG, Basel.

Prevalence and characterization of extended-spectrum-β-lactamase-producing Escherichia coli and Klebsiella pneumoniae in ready-to-eat vegetables.

PubMed

Kim, Hong-Seok; Chon, Jung-Whan; Kim, Young-Ji; Kim, Dong-Hyeon; Kim, Mu-sang; Seo, Kun-Ho

2015-08-17

The objective of this investigation was to determine the prevalence and characteristics of extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae in ready-to-eat (RTE) vegetables. A total of 189 RTE vegetable samples (91 sprouts and 98 mixed salads) were collected in a retail market in South Korea from October 2012 to February 2013. The prevalence of ESBL-producing E. coli and K. pneumoniae was 10.1%. Of these, 94.7% were from the sprout samples. All isolates were resistant to cefotaxime, and many of the ESBL producers were also resistant to non-β-lactam antibiotics, including gentamicin, trimethoprim/sulfamethoxazole, and ciprofloxacin (73.7%, 63.2%, and 26.3% respectively). TEM-1, SHV-1, -2, -11, -12, -27, -28 and -61, and CTX-M-14, -15 and -55 β-lactamases were detected alone or in combination. The genetic platforms of all CTX-M producing isolates were ISEcp1-blaCTX-M-orf477 and ISEcp1-blaCTX-M-IS903 in CTX-M groups 1 and 9, respectively. To our knowledge, this is the first report of the prevalence and characterization of ESBL-producing E. coli and K. pneumoniae isolated from RTE vegetables. The results of this study indicate that RTE vegetables, sprouts, in particular, may play a role in spreading antimicrobial resistant bacteria and ESBL genes to humans. Copyright © 2015 Elsevier B.V. All rights reserved.

Readiness and motivation for change among young women with broadly defined eating disorders.

PubMed

Ålgars, Monica; Ramberg, Carin; Moszny, Josefine; Hagman, Jessica; Rintala, Hanna; Santtila, Pekka

2015-01-01

Readiness and motivation for change were examined in 32 women with broadly defined eating disorders who took part in a 10-week Cognitive Behavioral Therapy (CBT)-based group intervention. Readiness for change and eating disorder psychopathology were assessed before and after the intervention. The results revealed significant negative associations between degree of eating disorder symptoms and degree of readiness for change before the intervention started. In particular, higher levels of eating concern, shape concern, and body dissatisfaction were associated with lower motivation for change. No significant associations between degree of readiness for change before the intervention started and changes in eating disorder symptoms at the end of intervention were found. Readiness for change increased from the beginning to the end of the intervention, indicating that group CBT may be a cost-effective and time-efficient way of enhancing readiness and motivation for change in individuals with eating psychopathology.

A practical implementation science heuristic for organizational readiness: R = MC2

PubMed Central

Cook, Brittany S.; Lamont, Andrea; Wandersman, Abraham; Castellow, Jennifer; Katz, Jason; Beidas, Rinad S.

2015-01-01

There are many challenges when an innovation (i.e., a program, process, or policy that is new to an organization) is actively introduced into an organization. One critical component for successful implementation is the organization’s readiness for the innovation. In this article, we propose a practical implementation science heuristic, abbreviated as R= MC2. We propose that organizational readiness involves: 1) the motivation to implement an innovation, 2) the general capacities of an organization, and 3) the innovation-specific capacities needed for a particular innovation. Each of these components can be assessed independently and be used formatively. The heuristic can be used by organizations to assess readiness to implement and by training and technical assistance providers to help build organizational readiness. We present an illustration of the heuristic by showing how behavioral health organizations differ in readiness to implement a peer specialist initiative. Implications for research and practice of organizational readiness are discussed. PMID:26668443

The Condition of College & Career Readiness 2016: New York Key Findings

ERIC Educational Resources Information Center

ACT, Inc., 2016

2016-01-01

"The Condition of College and Career Readiness" looks at the progress of the 2016 ACT®-tested graduating class relative to college and career readiness. This state briefing begins with statistics in the following categories for New York: performance, STEM, career readiness, impact, behaviors that impact access and opportunity, pipeline,…

Defining School Readiness in Maryland: A Multi-Dimensional Perspective. Publication #2012-44

ERIC Educational Resources Information Center

Forry, Nicole; Wessel, Julia

2012-01-01

Increased emphasis has been placed on children's ability to enter kindergarten ready to learn, a concept referred to as "school readiness." School readiness has been defined by the Maryland State Department of Education as "the stage of human development that enables a child to engage in, and benefit from, primary learning…

The Condition of College & Career Readiness 2016: West Virginia Key Findings

ERIC Educational Resources Information Center

ACT, Inc., 2016

2016-01-01

"The Condition of College and Career Readiness" looks at the progress of the 2016 ACT®-tested graduating class relative to college and career readiness. This state briefing begins with statistics in the following categories for West Virginia: performance, STEM, career readiness, impact, behaviors that impact access and opportunity,…

Technology Readiness of School Teachers: An Empirical Study of Measurement and Segmentation

ERIC Educational Resources Information Center

Badri, Masood; Al Rashedi, Asma; Yang, Guang; Mohaidat, Jihad; Al Hammadi, Arif

2014-01-01

The Technology Readiness Index (TRI) developed by Parasuraman (2000) was adapted to measure the technology readiness of public school teachers in Abu Dhabi, United Arab Emirates. The study aims at better understanding the factors (mostly demographics) that affect such readiness levels. In addition, Abu Dhabi teachers are segmented into five main…

The Condition of College & Career Readiness, 2011

ERIC Educational Resources Information Center

ACT, Inc., 2011

2011-01-01

Since 1959, ACT has collected and reported data on students' academic readiness for college. This report provides a college and career readiness snapshot of the ACT-tested high school class of 2011. ACT has long defined college and career readiness as the acquisition of the knowledge and skills a student needs to enroll and succeed in…

Reconceptualizing Dominant Discourses in Early Childhood Education: Exploring "Readiness" as an Active-Ethical-Relation

ERIC Educational Resources Information Center

Evans, Katherine

2015-01-01

This paper considers the landscape of early childhood education in England to be dominated by discourses of "readiness-for-school" and "readiness-for-learning" that act to heavily stratify the educational spaces inhabited by young children. The "ready-child" is constructed as a normative identity towards which the…

Thoughts on a Multidimensional Middle School Index of College Readiness

ERIC Educational Resources Information Center

Mattern, Krista; Allen, Jeff; Camara, Wayne

2016-01-01

The findings of the Gaertner and McClarty article (2015) raised awareness on two extremely important topics related to college readiness: First, to effect change, we must measure students' progression towards college readiness throughout their K-12 career rather than just at the culmination of high school. Second, college readiness encompasses…

The Condition of College & Career Readiness 2016: New Hampshire Key Findings

ERIC Educational Resources Information Center

ACT, Inc., 2016

2016-01-01

"The Condition of College and Career Readiness" looks at the progress of the 2016 ACT®-tested graduating class relative to college and career readiness. This state briefing begins with statistics in the following categories for New Hampshire: performance, STEM, career readiness, behaviors that impact access and opportunity, pipeline, and…

Necessary School Readiness Skills for Kindergarten Success According to Jordanian Teachers

ERIC Educational Resources Information Center

Abu Taleb, Tagreed Fathi

2013-01-01

The purpose of this study was to examine the necessity levels of children's school readiness skills held by Jordanian kindergarten teachers. The sample consisted of 347 teachers drawn from the public and private kindergarten education sectors. The school readiness data collection instrument included seven readiness domains with a total of 39…

75 FR 35458 - National Drinking Water Advisory Council's Climate Ready Water Utilities Working Group Meeting...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-22

... supportive environment in which a utility can take steps to be climate ready. In this meeting, the Working... Ready Water Utilities Working Group Meeting Announcement AGENCY: Environmental Protection Agency (EPA... fourth in-person meeting of the Climate Ready Water Utilities (CRWU) Working Group of the National...

78 FR 76710 - Notice of Buy America Waiver for a Video Ready Access Device Cabinet

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-18

... Buy America Waiver for a Video Ready Access Device Cabinet AGENCY: Federal Transit Administration, DOT... America waiver for a Video Ready Access Device (VRAD) cabinet, the Federal Transit Administration (FTA... Transit Administration (FTA) has granted a non- availability waiver for the procurement of a Video Ready...

The Condition of College & Career Readiness 2016: New Mexico Key Findings

ERIC Educational Resources Information Center

ACT, Inc., 2016

2016-01-01

"The Condition of College and Career Readiness" looks at the progress of the 2016 ACT®-tested graduating class relative to college and career readiness. This state briefing begins with statistics in the following categories for New Mexico: performance, STEM, career readiness, impact, behaviors that impact access and opportunity,…

Trends and Tensions: Australian and International Research about Starting School

ERIC Educational Resources Information Center

Dockett, Sue; Perry, Bob

2013-01-01

This paper details and compares the discernible trends observed in a wide-ranging review of the recent starting school literature in Australia and beyond. More than half of the research reviewed considers children's readiness for school. This research is critiqued through a three-way view of readiness: child readiness, school readiness and support…

Drinking and Dating: Examining the Link between Relationship Satisfaction, Hazardous Drinking, and Readiness-to-Change in College Dating Relationships

PubMed Central

Khaddouma, Alexander; Shorey, Ryan C.; Brasfield, Hope; Febres, Jeniimarie; Zapor, Heather; Elmquist, Joanna; Stuart, Gregory L.

2015-01-01

The present study examined the influence of relationship satisfaction on readiness-to-change alcohol use and the influence of hazardous drinking on readiness-to-change relationship issues in college student dating relationships. A sample of 219 college students in a current dating relationship (aged 18–25) completed self-report measures of dating relationship satisfaction, alcohol use, readiness-to-change alcohol use, and readiness-to-change relationship issues via an online survey from August to December 2011. Participants were grouped on the basis of their scores on measures of alcohol use (hazardous drinkers vs. nonhazardous drinkers) and relationship satisfaction (high vs. low). Results indicated that alcohol use was negatively correlated with relationship satisfaction. Furthermore, hazardous drinkers with high relationship satisfaction indicated more readiness-to-change alcohol use than hazardous drinkers with low relationship satisfaction. Alcohol problems were not related to readiness-to-change relationship issues. These findings indicate that highly satisfied dating relationships during college may positively influence readiness-to-change heavy drinking habits among college students. PMID:26997754

Life Cycle Cost Analysis of Ready Mix Concrete Plant

NASA Astrophysics Data System (ADS)

Topkar, V. M.; Duggar, A. R.; Kumar, A.; Bonde, P. P.; Girwalkar, R. S.; Gade, S. B.

2013-11-01

India, being a developing nation is experiencing major growth in its infrastructural sector. Concrete is the major component in construction. The requirement of good quality of concrete in large quantities can be fulfilled by ready mix concrete batching and mixing plants. The paper presents a technique of applying the value engineering tool life cycle cost analysis to a ready mix concrete plant. This will help an investor or an organization to take investment decisions regarding a ready mix concrete facility. No economic alternatives are compared in this study. A cost breakdown structure is prepared for the ready mix concrete plant. A market survey has been conducted to collect realistic costs for the ready mix concrete facility. The study establishes the cash flow for the ready mix concrete facility helpful in investment and capital generation related decisions. Transit mixers form an important component of the facility and are included in the calculations. A fleet size for transit mixers has been assumed for this purpose. The life cycle cost has been calculated for the system of the ready mix concrete plant and transit mixers.

a Simple Symmetric Algorithm Using a Likeness with Introns Behavior in RNA Sequences

NASA Astrophysics Data System (ADS)

Regoli, Massimo

2009-02-01

The RNA-Crypto System (shortly RCS) is a symmetric key algorithm to cipher data. The idea for this new algorithm starts from the observation of nature. In particular from the observation of RNA behavior and some of its properties. The RNA sequences has some sections called Introns. Introns, derived from the term "intragenic regions", are non-coding sections of precursor mRNA (pre-mRNA) or other RNAs, that are removed (spliced out of the RNA) before the mature RNA is formed. Once the introns have been spliced out of a pre-mRNA, the resulting mRNA sequence is ready to be translated into a protein. The corresponding parts of a gene are known as introns as well. The nature and the role of Introns in the pre-mRNA is not clear and it is under ponderous researches by Biologists but, in our case, we will use the presence of Introns in the RNA-Crypto System output as a strong method to add chaotic non coding information and an unnecessary behaviour in the access to the secret key to code the messages. In the RNA-Crypto System algoritnm the introns are sections of the ciphered message with non-coding information as well as in the precursor mRNA.

A multi-country outbreak of Salmonella Newport gastroenteritis in Europe associated with watermelon from Brazil, confirmed by whole genome sequencing: October 2011 to January 2012.

PubMed

Byrne, L; Fisher, I; Peters, T; Mather, A; Thomson, N; Rosner, B; Bernard, H; McKeown, P; Cormican, M; Cowden, J; Aiyedun, V; Lane, C

2014-08-07

In November 2011, the presence of Salmonella Newport in a ready-to-eat watermelon slice was confirmed as part of a local food survey in England. In late December 2011, cases of S. Newport were reported in England, Wales, Northern Ireland, Scotland, Ireland and Germany. During the outbreak, 63 confirmed cases of S. Newport were reported across all six countries with isolates indistinguishable by pulsed-field gel electrophoresis from the watermelon isolate.A subset of outbreak isolates were whole-genome sequenced and were identical to, or one single nucleotide polymorphism different from the watermelon isolate.In total, 46 confirmed cases were interviewed of which 27 reported watermelon consumption. Further investigations confirmed the outbreak was linked to the consumption of watermelon imported from Brazil.Although numerous Salmonella outbreaks associated with melons have been reported in the United States and elsewhere, this is the first of its kind in Europe.Expansion of the melon import market from Brazil represents a potential threat for future outbreaks. Whole genome sequencing is rapidly becoming more accessible and can provide a compelling level of evidence of linkage between human cases and sources of infection,to support public health interventions in global food markets.

A multi-country outbreak of Salmonella Newport gastroenteritis in Europe associated with watermelon from Brazil, confirmed by whole genome sequencing: October 2011 to January 2012

PubMed Central

Byrne, L; Fisher, I; Peters, T; Mather, A; Thomson, N; Rosner, B; Bernard, H; McKeown, P; Cormican, M; Cowden, J; Aiyedun, V; Lane, C

2015-01-01

In November 2011, the presence of Salmonella Newport in a ready-to-eat watermelon slice was confirmed as part of a local food survey in England. In late December 2011, cases of S. Newport were reported in England, Wales, Northern Ireland, Scotland, Ireland and Germany. During the outbreak, 63 confirmed cases of S. Newport were reported across all six countries with isolates indistinguishable by pulsed-field gel electrophoresis from the watermelon isolate. A subset of outbreak isolates were whole-genome sequenced and were identical to, or one single nucleotide polymorphism different from the watermelon isolate. In total, 46 confirmed cases were interviewed of which 27 reported watermelon consumption. Further investigations confirmed the outbreak was linked to the consumption of watermelon imported from Brazil. Although numerous Salmonella outbreaks associated with melons have been reported in the United States and elsewhere, this is the first of its kind in Europe. Expansion of the melon import market from Brazil represents a potential threat for future outbreaks. Whole genome sequencing is rapidly becoming more accessible and can provide a compelling level of evidence of linkage between human cases and sources of infection, to support public health interventions in global food markets. PMID:25138971

Enzymatic synthesis of random sequences of RNA and RNA analogues by DNA polymerase theta mutants for the generation of aptamer libraries.

PubMed

Randrianjatovo-Gbalou, Irina; Rosario, Sandrine; Sismeiro, Odile; Varet, Hugo; Legendre, Rachel; Coppée, Jean-Yves; Huteau, Valérie; Pochet, Sylvie; Delarue, Marc

2018-05-21

Nucleic acid aptamers, especially RNA, exhibit valuable advantages compared to protein therapeutics in terms of size, affinity and specificity. However, the synthesis of libraries of large random RNAs is still difficult and expensive. The engineering of polymerases able to directly generate these libraries has the potential to replace the chemical synthesis approach. Here, we start with a DNA polymerase that already displays a significant template-free nucleotidyltransferase activity, human DNA polymerase theta, and we mutate it based on the knowledge of its three-dimensional structure as well as previous mutational studies on members of the same polA family. One mutant exhibited a high tolerance towards ribonucleotides (NTPs) and displayed an efficient ribonucleotidyltransferase activity that resulted in the assembly of long RNA polymers. HPLC analysis and RNA sequencing of the products were used to quantify the incorporation of the four NTPs as a function of initial NTP concentrations and established the randomness of each generated nucleic acid sequence. The same mutant revealed a propensity to accept other modified nucleotides and to extend them in long fragments. Hence, this mutant can deliver random natural and modified RNA polymers libraries ready to use for SELEX, with custom lengths and balanced or unbalanced ratios.

SparkSeq: fast, scalable and cloud-ready tool for the interactive genomic data analysis with nucleotide precision.

PubMed

Wiewiórka, Marek S; Messina, Antonio; Pacholewska, Alicja; Maffioletti, Sergio; Gawrysiak, Piotr; Okoniewski, Michał J

2014-09-15

Many time-consuming analyses of next -: generation sequencing data can be addressed with modern cloud computing. The Apache Hadoop-based solutions have become popular in genomics BECAUSE OF: their scalability in a cloud infrastructure. So far, most of these tools have been used for batch data processing rather than interactive data querying. The SparkSeq software has been created to take advantage of a new MapReduce framework, Apache Spark, for next-generation sequencing data. SparkSeq is a general-purpose, flexible and easily extendable library for genomic cloud computing. It can be used to build genomic analysis pipelines in Scala and run them in an interactive way. SparkSeq opens up the possibility of customized ad hoc secondary analyses and iterative machine learning algorithms. This article demonstrates its scalability and overall fast performance by running the analyses of sequencing datasets. Tests of SparkSeq also prove that the use of cache and HDFS block size can be tuned for the optimal performance on multiple worker nodes. Available under open source Apache 2.0 license: https://bitbucket.org/mwiewiorka/sparkseq/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Repetition as the essence of life on this earth: music and genes.

PubMed

Ohno, S

1987-01-01

In prebiotic nucleic acid replication, templates appear to have been in short supply. A single round of tandem duplication of existing oligomers assured progressive extension of templates to the length adequate for encoding of polypeptide chains. Thus, the first set of coding sequences had to be repeats of base oligomers encoding polypeptide chains of various periodicities. On one hand, the readiness of these periodical polypeptide chains to assume alpha-helical and/or beta-sheet secondary structures contributed to the extremely rapid initial functional diversification of these polypeptide chains. It would be recalled that most, if not all, of the sugar-metabolizing enzymes had already achieved the inviolable functional competence before the division of prokaryotes from eukaryotes. On the other hand, a certain (dipeptidic?) of the peptidic periodicities was apparently chosen as the timekeeping unit by the biological clock. Musical compositions too apparently evolved originally as a timekeeping device. Accordingly, repetitiousness is evident in all musical compositions. Evolution of musical compositions from the early Baroque to the late Romantic parallels that of coding sequences from rather exact repeats of base oligomers to more complex modern coding sequences in which repetitious elements are less conspicuous and more varied. Inasmuch as the earth is governed by the hierarchy of periodicities (days, months and years), such reliance on periodicities is rather expected.

Consumer behaviors towards ready-to-eat foods based on food-related lifestyles in Korea

PubMed Central

Bae, Hyun-Joo; Chae, Mi-Jin

2010-01-01

The purpose of this study was to examine consumers' behaviors toward ready-to-eat foods and to develop ready-to-eat food market segmentation in Korea. The food-related lifestyle and purchase behaviors of ready-to-eat foods were evaluated using 410 ready-to-eat food consumers in the Republic of Korea. Four factors were extracted by exploratory factor analysis (health-orientation, taste-orientation, convenience-orientation, and tradition-orientation) to explain the ready-to eat food consumers' food-related lifestyles. The results of cluster analysis indicated that "tradition seekers" and "convenience seekers" should be regarded as the target segments. Chi-square tests and t-tests of the subdivided groups showed there were significant differences across marital status, education level, family type, eating-out expenditure, place of purchase, and reason for purchase. In conclusion, the tradition seekers consumed more ready-to-eat foods from discount marts or specialty stores and ate them between meals more often than the convenience seekers. In contrast, the convenience seekers purchased more ready-to-eat foods at convenience stores and ate them as meals more often than the tradition seekers. These findings suggest that ready-to-eat food market segmentation based on food-related lifestyles can be applied to develop proper marketing strategies. PMID:20827350

Consumer behaviors towards ready-to-eat foods based on food-related lifestyles in Korea.

PubMed

Bae, Hyun-Joo; Chae, Mi-Jin; Ryu, Kisang

2010-08-01

The purpose of this study was to examine consumers' behaviors toward ready-to-eat foods and to develop ready-to-eat food market segmentation in Korea. The food-related lifestyle and purchase behaviors of ready-to-eat foods were evaluated using 410 ready-to-eat food consumers in the Republic of Korea. Four factors were extracted by exploratory factor analysis (health-orientation, taste-orientation, convenience-orientation, and tradition-orientation) to explain the ready-to eat food consumers' food-related lifestyles. The results of cluster analysis indicated that "tradition seekers" and "convenience seekers" should be regarded as the target segments. Chi-square tests and t-tests of the subdivided groups showed there were significant differences across marital status, education level, family type, eating-out expenditure, place of purchase, and reason for purchase. In conclusion, the tradition seekers consumed more ready-to-eat foods from discount marts or specialty stores and ate them between meals more often than the convenience seekers. In contrast, the convenience seekers purchased more ready-to-eat foods at convenience stores and ate them as meals more often than the tradition seekers. These findings suggest that ready-to-eat food market segmentation based on food-related lifestyles can be applied to develop proper marketing strategies.

Strategies to Build Readiness in Community Mobilization Efforts for Implementation in a Multi-Year Teen Pregnancy Prevention Initiative.

PubMed

Bhuiya, Nazmim; House, L Duane; Desmarais, Jeffrey; Fletcher, Erica; Conlin, Maeve; Perez-McAdoo, Sarah; Waggett, Jessica; Tendulkar, Shalini A

2017-03-01

This paper describes an assessment of community readiness to implement a community-wide teen pregnancy prevention initiative, Youth First, and presents strategies used to enhance this readiness as informed by the assessment. Twenty-five community stakeholder interviews were conducted to assess four domains of readiness: (1) attitudes, perception, and knowledge of teen pregnancy; (2) perceived level of readiness; (3) resources, existing and current efforts; and (4) leadership. Interview transcripts were coded and analyzed to identify key themes. Stakeholders acknowledged teen pregnancy as an issue but lacked contextual information. They also perceived the community as ready to address the issue and recognized some organizations already championing efforts. However, many key players were not involved, and ongoing data collection to assess teen pregnancy and prevention efforts was limited. Though many stakeholders were ready to engage in teen pregnancy prevention efforts, they required additional information and training to appropriately address the issue. In response to the assessment findings, several strategies were applied to address readiness and build Youth First partners' capacity to implement the community-wide initiative. Thus, to successfully implement community-wide prevention efforts, it is valuable to assess the level of community readiness to address health issues. Copyright © 2016 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

Analysis of e-learning implementation readiness based on integrated elr model

NASA Astrophysics Data System (ADS)

Adiyarta, K.; Napitupulu, D.; Rahim, R.; Abdullah, D.; Setiawan, MI

2018-04-01

E-learning nowadays has become a requirement for institutions to support their learning activities. To adopt e-learning, an institution requires a large strategy and resources for optimal application. Unfortunately, not all institutions that have used e-learning got the desired results or expectations. This study aims to identify the extent of the level of readiness of e-learning implementation in institution X. The degree of institutional readiness will determine the success of future e-learning utilization. In addition, institutional readiness measurement are needed to evaluate the effectiveness of strategies in e-learning development. The research method used is survey with questionnaire designed based on integration of 8 best practice ELR (e-learning readiness) model. The results showed that from 13 factors of integrated ELR model being measured, there are 3 readiness factors included in the category of not ready and needs a lot of work. They are human resource (2.57), technology skill (2.38) and content factors (2.41). In general, e-learning implementation in institutions is in the category of not ready but needs some of work (3.27). Therefore, the institution should consider which factors or areas of ELR factors are considered still not ready and needs improvement in the future.

Changing Community Readiness To Prevent The Abuse Of Inhalants And Other Harmful Legal Products In Alaska1

PubMed Central

Ogilvie, Kristen A.; Moore, Roland S.; Ogilvie, Diane C.; Johnson, Knowlton W.; Collins, David A.; Shamblen, Stephen R.

2008-01-01

This paper presents results from an application of the Community Readiness Model (CRM) as part of a multi-stage community mobilization strategy to engage community leaders, retailers, parents, and school personnel in preventing youth use of inhalants and other harmful legal products in rural Alaska. The CRM is designed to assess readiness to address a single social problem, based on a limited set of key informant interviews. In this study, researchers conducted 32 baseline and 34 post-intervention community readiness assessment interviews in four rural Alaskan communities. These interviews with key informants from the communities were coded and analyzed using CRM methods to yield readiness scores for each community. The aggregate results were analyzed using hierarchical linear modeling (HLM), and the individual community scores were analyzed in the context of the overall study. Significant positive changes in community readiness were found across six readiness dimensions as well as for the overall readiness score. Variation in the degree of changes in readiness across the four communities is attributed to differences in the intervention’s implementation. The implications of these results include the potential for CRM assessments to serve as an integral component of a community mobilization strategy and also to offer meaningful feedback to communities participating in prevention research. PMID:18392927

[Genetic characterization and antimicrobial susceptibility analysis of methicillin-resistant Staphylococcus aureus isolated from ready-to-eat food and pig-related sources in China].

PubMed

Wang, Wei; Guo, Yunchang; Pei, Xiaoyan; Hu, Yujie; Bai, Li; Sun, Aiping; Liu, Jikai; Fu, Ping; Li, Fengqin

2013-11-01

To study the mecA gene distribution in 877 strains of Staphylococcus aureus isolated from the environment of pig farm and slaughter house, pig carcass and its iliac lymph nodes, and ready-to-eat foods in China as to screen the methicillin-resistant Staphylococcus aureus (MRSA), and to evaluate the antimicrobial susceptibility of MRSA. A total of 877 strains of S. aureus that had been phenotypically identified by Gram staining, catalase test, ability to coagulate rabbit plasma, API STAPH as well as analysis of nuc gene, encoding for a S. aureus specific thermonu-clease were screened for MRSA by characterizing the mecA gene. The antimicrobial susceptibility of MRSA was tested in accordance with the broth microdilution method recommended by the Clinical and Laboratory Standards Institute. Of 877 S. aureus strains tested, 71 (8.1%, 71/887) were mecA positive and identified as MRSA, among which, 48 isolates were pig-associated and 23 isolates were ready-to-eat food-associated. The frequency of pig-associated MRSA was significantly higher than that of food-associated one (chi2 = 53.040, P < 0.01). All MRSA were susceptible to linezolid, vancomycin, tigecycline, and nitrofurantoin but resistant to cefoxitin, oxacillin and benzylpenicillin. Meanwhile, 98.6% (70 strains), 95.8% (68 strains), 88.7% (63 strains), 80.3% (57 strains), 80.3% (57 strains) and 32.4% (23 strains) MRSA exhibited the resistance to clindamycin, erythromycin, tetracycline, ciprofloxacin, trimethoprim/sulfamethoxazole, and gentamicin, respectively. Besides, one strain was resistant to each of antibiotics including levofloxacin, moxifloxacin, rifampicin, and quinupristin/dalfopristin. It was worth noting that the frequency of resistance to ciprofloxacin, tetracycline, and trimethoprim/sulfamethoxazole of pig-associated MRSA was significantly higher than that of food-associated MRSA (CIP: chi2 = 29.110, P < 0.01, TET: chi2 = 18.816, P < 0.01, TMP/ SMZ: chi2 = 36.394, P < 0.01). It should be pointed out that 70 (98.6%) strains of MRSA were multi-drug resistant and eight spectrums of antimicrobial susceptibility were observed. The multi-drug resistant MRSA isolated from pig- and food-associated matrixin China is very serious.

Development and pilot-test of the Workplace Readiness Questionnaire, a theory-based instrument to measure small workplaces’ readiness to implement wellness programs

PubMed Central

Hannon, Peggy A.; Helfrich, Christian D.; Chan, K. Gary; Allen, Claire L.; Hammerback, Kristen; Kohn, Marlana J.; Parrish, Amanda T.; Weiner, Bryan J.; Harris, Jeffrey R.

2016-01-01

Purpose To develop a theory-based questionnaire to assess readiness for change in small workplaces adopting wellness programs. Design In developing our scale, we first tested items via “think-aloud” interviews. We tested the revised items in a cross-sectional quantitative telephone survey. Setting Small workplaces (20–250 employees) in low-wage industries. Subjects Decision-makers representing small workplaces in King County, Washington (think-aloud interviews, n=9) and the United States (telephone survey, n=201). Measures We generated items for each construct in Weiner’s theory of organizational readiness for change. We also measured workplace characteristics and current implementation of workplace wellness programs. Analysis We assessed reliability by coefficient alpha for each of the readiness questionnaire subscales. We tested the association of all subscales with employers’ current implementation of wellness policies, programs, and communications, and conducted a path analysis to test the associations in the theory of organizational readiness to change. Results Each of the readiness subscales exhibited acceptable internal reliability (coefficient alpha range = .75–.88) and was positively associated with wellness program implementation (p <.05). The path analysis was consistent with the theory of organizational readiness to change, except change efficacy did not predict change-related effort. Conclusion We developed a new questionnaire to assess small workplaces’ readiness to adopt and implement evidence-based wellness programs. Our findings also provide empirical validation of Weiner’s theory of readiness for change. PMID:26389975

SaludABLEOmaha: Improving Readiness to Address Obesity Through Healthy Lifestyle in a Midwestern Latino Community, 2011–2013

PubMed Central

Frerichs, Leah; Brittin, Jeri; Robbins, Regina; Steenson, Sharalyn; Stewart, Catherine; Fisher, Christopher

2015-01-01

Background A community’s readiness for change is a precursor to the effective application of evidence-based practices for health promotion. Research is lacking regarding potential strategies to improve readiness to address obesity-related health issues in underserved communities. Community Context This case study describes SaludABLEOmaha, an initiative to increase readiness of residents in a Midwestern Latino community to address obesity and adopt healthy lifestyles. Methods SaludABLEOmaha emphasized 2 core approaches, youth activism and collaboration among public and private institutions, which we applied to planning and implementing tactics in support of 3 interconnected strategies: 1) social marketing and social media, 2) service learning in schools (ie, curricula that integrate hands-on community service with instruction and reflection), and 3) community and business engagement. Following the Community Readiness Model protocol (http://triethniccenter.colostate.edu/communityReadiness.htm), structured interviews were conducted with community leaders and analyzed before and 2.5 years after launch of the program. Outcome The community increased in readiness from stage 3 of the Community Readiness Model, “vague awareness,” at baseline to stage 5, “preparation,” at follow-up. Interpretation SaludABLEOmaha improved community readiness (eg, community knowledge, community climate), which probably contributed to the observed increase in readiness to address obesity through healthy lifestyle. Community mobilization approaches such as youth activism integrated with social marketing and social media tactics can improve community responsiveness to obesity prevention and diminish health disparities. PMID:25674679

Development and Pilot Test of the Workplace Readiness Questionnaire, a Theory-Based Instrument to Measure Small Workplaces' Readiness to Implement Wellness Programs.

PubMed

Hannon, Peggy A; Helfrich, Christian D; Chan, K Gary; Allen, Claire L; Hammerback, Kristen; Kohn, Marlana J; Parrish, Amanda T; Weiner, Bryan J; Harris, Jeffrey R

2017-01-01

To develop a theory-based questionnaire to assess readiness for change in small workplaces adopting wellness programs. In developing our scale, we first tested items via "think-aloud" interviews. We tested the revised items in a cross-sectional quantitative telephone survey. The study setting comprised small workplaces (20-250 employees) in low-wage industries. Decision-makers representing small workplaces in King County, Washington (think-aloud interviews, n = 9), and the United States (telephone survey, n = 201) served as study subjects. We generated items for each construct in Weiner's theory of organizational readiness for change. We also measured workplace characteristics and current implementation of workplace wellness programs. We assessed reliability by coefficient alpha for each of the readiness questionnaire subscales. We tested the association of all subscales with employers' current implementation of wellness policies, programs, and communications, and conducted a path analysis to test the associations in the theory of organizational readiness to change. Each of the readiness subscales exhibited acceptable internal reliability (coefficient alpha range, .75-.88) and was positively associated with wellness program implementation ( p < .05). The path analysis was consistent with the theory of organizational readiness to change, except change efficacy did not predict change-related effort. We developed a new questionnaire to assess small workplaces' readiness to adopt and implement evidence-based wellness programs. Our findings also provide empirical validation of Weiner's theory of readiness for change.

Consumption of ready-made meals and increased risk of obesity: findings from the Observation of Cardiovascular Risk Factors in Luxembourg (ORISCAV-LUX) study.

PubMed

Alkerwi, Ala'a; Crichton, Georgina E; Hébert, James R

2015-01-28

The consumption of ready-made meals, such as pre-packaged dishes, available at grocery stores and fast-food restaurants, is a habit related to our modern fast-paced lives. No study has examined the association of daily ready-made meal consumption with diet quality or health-related outcomes. The present study aimed to investigate the association between self-reported ready-made meal consumption and diet quality, as measured by compliance with dietary recommendations and with a set of adiposity measures, in a nationally representative sample of 1352 subjects, aged 18-69 years, participating in the nationwide population-based ORISCAV-LUX (Observation of Cardiovascular Risk Factors in Luxembourg) survey. The daily consumption of ready-made meals was calculated as follows: frequency of consumption × portion size × number of portions consumed. The sum of the daily consumption values of the eleven pre-packaged dishes included in the FFQ represented the total daily consumption of ready-made meals (g/d) for each participant. About 97% of the participants reported daily consumption of ready-made meals. The intake was highly prevalent in men living alone and varied according to education level. Ready-made meal consumption provided >7% of total daily energy. The fractions (%) of macro- and micronutrients derived from daily consumption of ready-made meals varied from 10% for total cholesterol to 0.65% for total fibre. Increased consumption of ready-made meals was found to be independently associated with abdominal obesity. On controlling for age, sex, socio-economic status and lifestyle factors, daily consumption of ready-made meals was found to be associated with higher energy intake and with poor compliance with national nutritional recommendations, and hence it could plausibly increase the risk of central obesity and fat deposition.

Are you ready? Exploring readiness to engage in exercise among people living with HIV and multimorbidity in Toronto, Canada: a qualitative study

PubMed Central

Simonik, Alya; Vader, Kyle; Ellis, Denine; Kesbian, Dirouhi; Leung, Priscilla; Jachyra, Patrick; Chan Carusone, Soo; O'Brien, Kelly K

2016-01-01

Objectives Our aim was to explore readiness to engage in exercise among people living with HIV and multimorbidity. Design We conducted a descriptive qualitative study using face-to-face semistructured interviews with adults living with HIV. Setting We recruited adults (18 years or older) who self-identified as living with HIV and 2 or more additional health-related conditions from a specialty hospital in Toronto, Canada. Participants 14 participants with a median age of 50 years and median number of 9 concurrent health-related conditions participated in the study. The majority of participants were men (64%) with an undetectable viral load (71%). Outcome measures We asked participants to describe their readiness to engage in exercise and explored how contextual factors influenced their readiness. We analysed interview transcripts using thematic analysis. Results We developed a framework to describe readiness to engage in exercise and the interplay of factors and their influence on readiness among adults with HIV and multimorbidity. Readiness was described as a diverse, dynamic and fluctuating spectrum ranging from not thinking about exercise to routinely engaging in daily exercise. Readiness was influenced by the complex and episodic nature of HIV and multimorbidity comprised of physical impairments, mental health challenges and uncertainty from HIV and concurrent health conditions. This key factor created a context within which 4 additional subfactors (social supports, perceptions and beliefs, past experience with exercise, and accessibility) may further hinder or facilitate an individual's position along the spectrum of readiness to exercise. Conclusions Readiness to engage in exercise among people living with HIV is a dynamic and fluctuating construct that may be influenced by the episodic nature of HIV and multimorbidity and 4 subfactors. Strategies to facilitate readiness to exercise should consider the interplay of these factors in order to enhance physical activity and subsequently improve health outcomes of people with HIV and multimorbidity. PMID:26956163

An image processing study of a reentrant discotic cholesteric - biaxial cholesteric phase transition

NASA Astrophysics Data System (ADS)

Luders, D. D.; Zoner, G. A.; Santos, O. R.; Braga, W. S.; Sampaio, A. R.; Kimura, N. M.; Palangana, A. J.; Simões, M.

2018-04-01

In this work, we study and characterize the cholesteric sequence of phases (ChDr - ChB - ChD), where the first ChDr is the reentrant cholesteric discotic phase, ChB is the cholesteric biaxial phase and the second ChD is the cholesteric discotic phase. This sequence of phases is studied through polarized light microscopy and image processing technique, where, for the first time, the domains and borders of these transitions are established and characterized. They are also investigated and optically characterized throughout their textures.

A theory of organizational readiness for change

PubMed Central

Weiner, Bryan J

2009-01-01

Background Change management experts have emphasized the importance of establishing organizational readiness for change and recommended various strategies for creating it. Although the advice seems reasonable, the scientific basis for it is limited. Unlike individual readiness for change, organizational readiness for change has not been subject to extensive theoretical development or empirical study. In this article, I conceptually define organizational readiness for change and develop a theory of its determinants and outcomes. I focus on the organizational level of analysis because many promising approaches to improving healthcare delivery entail collective behavior change in the form of systems redesign--that is, multiple, simultaneous changes in staffing, work flow, decision making, communication, and reward systems. Discussion Organizational readiness for change is a multi-level, multi-faceted construct. As an organization-level construct, readiness for change refers to organizational members' shared resolve to implement a change (change commitment) and shared belief in their collective capability to do so (change efficacy). Organizational readiness for change varies as a function of how much organizational members value the change and how favorably they appraise three key determinants of implementation capability: task demands, resource availability, and situational factors. When organizational readiness for change is high, organizational members are more likely to initiate change, exert greater effort, exhibit greater persistence, and display more cooperative behavior. The result is more effective implementation. Summary The theory described in this article treats organizational readiness as a shared psychological state in which organizational members feel committed to implementing an organizational change and confident in their collective abilities to do so. This way of thinking about organizational readiness is best suited for examining organizational changes where collective behavior change is necessary in order to effectively implement the change and, in some instances, for the change to produce anticipated benefits. Testing the theory would require further measurement development and careful sampling decisions. The theory offers a means of reconciling the structural and psychological views of organizational readiness found in the literature. Further, the theory suggests the possibility that the strategies that change management experts recommend are equifinal. That is, there is no 'one best way' to increase organizational readiness for change. PMID:19840381

Ready, Set, Change! Development and usability testing of an online readiness for change decision support tool for healthcare organizations.

PubMed

Timmings, Caitlyn; Khan, Sobia; Moore, Julia E; Marquez, Christine; Pyka, Kasha; Straus, Sharon E

2016-02-24

To address challenges related to selecting a valid, reliable, and appropriate readiness assessment measure in practice, we developed an online decision support tool to aid frontline implementers in healthcare settings in this process. The focus of this paper is to describe a multi-step, end-user driven approach to developing this tool for use during the planning stages of implementation. A multi-phase, end-user driven approach was used to develop and test the usability of a readiness decision support tool. First, readiness assessment measures that are valid, reliable, and appropriate for healthcare settings were identified from a systematic review. Second, a mapping exercise was performed to categorize individual items of included measures according to key readiness constructs from an existing framework. Third, a modified Delphi process was used to collect stakeholder ratings of the included measures on domains of feasibility, relevance, and likelihood to recommend. Fourth, two versions of a decision support tool prototype were developed and evaluated for usability. Nine valid and reliable readiness assessment measures were included in the decision support tool. The mapping exercise revealed that of the nine measures, most measures (78 %) focused on assessing readiness for change at the organizational versus the individual level, and that four measures (44 %) represented all constructs of organizational readiness. During the modified Delphi process, stakeholders rated most measures as feasible and relevant for use in practice, and reported that they would be likely to recommend use of most measures. Using data from the mapping exercise and stakeholder panel, an algorithm was developed to link users to a measure based on characteristics of their organizational setting and their readiness for change assessment priorities. Usability testing yielded recommendations that were used to refine the Ready, Set, Change! decision support tool . Ready, Set, Change! decision support tool is an implementation support that is designed to facilitate the routine incorporation of a readiness assessment as an early step in implementation. Use of this tool in practice may offer time and resource-saving implications for implementation.

Career readiness in adult survivors of childhood cancer: a report from the St. Jude Lifetime Cohort study

PubMed Central

Strauser, David; Klosky, James L.; Brinkman, Tara M.; Wong, Alex W.K.; Chan, Fong; Lanctot, Jennifer Q.; Ojha, Rohit P.; Robison, Leslie L.; Hudson, Melissa M.; Ness, Kirsten K.

2014-01-01

Purpose Adult survivors of childhood cancer experience difficulties in obtaining and maintaining employment. Employment-related challenges are associated with treatment-related health conditions, and may also be related to vocational factors such as career readiness, skill acquisition, and work experience. Unfortunately, little is known about how treatment, health and vocational related factors interact to impact career development among childhood cancer survivors. Methods 385 adult survivors of childhood cancer (42.1% male, median age 38 (21-62) years), participating in the St. Jude Lifetime Cohort study, completed a work experiences survey that included measures of career readiness and vocational identity. Logistic regression was used to compare characteristics of survivors in the low career readiness category to those in the medium or high career readiness category, and structural equation modeling (SEM) was utilized to evaluate associations between career readiness, vocational identity, treatment intensity and physical/emotional health. Results Low career readiness was prevalent in 17.4% of survivors. Univariate analysis did not identify any significant associations between cancer treatment-related factors and career readiness. Unemployed survivors (Odds ratio (OR) 2.3, 95% Confidence Interval (CI) 1.2-4.5), those who were not college graduates (OR 3.0, 95% CI 1.6-5.6), and those who had no personal income (OR 5.9, 95% CI 1.7-30.9) were at increased risk of low career readiness. SEM indicated that associations between treatment intensity, physical health, age at diagnosis and career readiness were mediated by emotional health and vocational identity. 63%, 35%, and 10% of the variance in career readiness, vocational identity, and emotional health, respectively, were explained by this theoretical model. Conclusions The results of this study indicate that individuals who reported low levels of career readiness were more likely to be unemployed, earn less than $40,000 per year, and were less likely to graduate from high school. The final structural model indicates that vocational identity and emotional health accounted for the indirect effect of treatment intensity, age a diagnosis, and physical health on career readiness. Implications for Cancer Survivors Addressing career readiness may be important to improve employment outcomes for adult survivors of childhood cancer. PMID:25047713

Characterization of circulating transfer RNA-derived RNA fragments in cattle

PubMed Central

Casas, Eduardo; Cai, Guohong; Neill, John D.

2015-01-01

The objective was to characterize naturally occurring circulating transfer RNA-derived RNA fragments (tRFs) in cattle1. Serum from eight clinically normal adult dairy cows was collected, and small non-coding RNAs were extracted immediately after collection and sequenced by Illumina MiSeq. Sequences aligned to transfer RNA (tRNA) genes or their flanking sequences were characterized. Sequences aligned to the beginning of 5′ end of the mature tRNA were classified as tRF5; those aligned to the 3′ end of mature tRNA were classified as tRF3; and those aligned to the beginning of the 3′ end flanking sequences were classified as tRF1. There were 3,190,962 sequences that mapped to transfer RNA and small non-coding RNAs in the bovine genome. Of these, 2,323,520 were identified as tRF5s, 562 were tRF3s, and 81 were tRF1s. There were 866,799 sequences identified as other small non-coding RNAs (microRNA, rRNA, snoRNA, etc.) and were excluded from the study. The tRF5s ranged from 28 to 40 nucleotides; and 98.7% ranged from 30 to 34 nucleotides in length. The tRFs with the greatest number of sequences were derived from tRNA of histidine, glutamic acid, lysine, glycine, and valine. There was no association between number of codons for each amino acid and number of tRFs in the samples. The reason for tRF5s being the most abundant can only be explained if these sequences are associated with function within the animal. PMID:26379699

An Hybrid Glass/hemp Fibers Solution Frp Pipes: Technical and Economic Advantages of Hand Lay up VS Light Rtm

NASA Astrophysics Data System (ADS)

Cicala, G.; Cristaldi, G.; Recca, G.; Ziegmann, G.; ElSabbagh, A.; Dickert, M.

2008-08-01

The aim of the present research was to investigate the replacement of glass fibers with hemp fibers for applications in the piping industry. The choice of hemp fibers was mainly related to the needs, expressed by some companies operating in this sector, for cost reduction without adversely reducing the performances of the pipes. Two processing techniques, namely hand lay up and light RTM, were evaluated. The pipe selected for the study was a curved fitting (90°) flanged at both ends. The fitting must withstand an internal pressure of 10 bar and the presence of acid aqueous solutions. The original lay-up used to build the pipe is a sequence of C-glass, glass mats and glass fabric. Commercial epoxy vinyl ester resin was used as thermoset matrix. Hemp fibers mats were selected as potential substitute of glass fibers mats because of their low cost and ready availability from different commercial sources. The data obtained from the mechanical characterization were used to define a favorable design of the pipe using hemp mats as internal layer. The proposed design for the fittings allowed for a cost reduction of about 24% and a weight saving of about 23% without any drawback in terms of the final performances. The light RTM techniques was developed on purpose for the manufacturing of the curved pipe. The comparison between hand lay up and light RTM evidenced a substantial cost reduction when light RTM was used.

AN HYBRID GLASS/HEMP FIBERS SOLUTION FRP PIPES: TECHNICAL AND ECONOMIC ADVANTAGES OF HAND LAY UP VS LIGHT RTM

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

Cicala, G.; Cristaldi, G.; Recca, G.

2008-08-28

The aim of the present research was to investigate the replacement of glass fibers with hemp fibers for applications in the piping industry. The choice of hemp fibers was mainly related to the needs, expressed by some companies operating in this sector, for cost reduction without adversely reducing the performances of the pipes. Two processing techniques, namely hand lay up and light RTM, were evaluated. The pipe selected for the study was a curved fitting (90 deg.) flanged at both ends. The fitting must withstand an internal pressure of 10 bar and the presence of acid aqueous solutions. The originalmore » lay-up used to build the pipe is a sequence of C-glass, glass mats and glass fabric. Commercial epoxy vinyl ester resin was used as thermoset matrix.Hemp fibers mats were selected as potential substitute of glass fibers mats because of their low cost and ready availability from different commercial sources. The data obtained from the mechanical characterization were used to define a favorable design of the pipe using hemp mats as internal layer. The proposed design for the fittings allowed for a cost reduction of about 24% and a weight saving of about 23% without any drawback in terms of the final performances.The light RTM techniques was developed on purpose for the manufacturing of the curved pipe. The comparison between hand lay up and light RTM evidenced a substantial cost reduction when light RTM was used.« less

Single Mode, Extreme Precision Doppler Spectrographs

NASA Astrophysics Data System (ADS)

Schwab, Christian; Leon-Saval, Sergio G.; Betters, Christopher H.; Bland-Hawthorn, Joss; Mahadevan, Suvrath

2014-04-01

The `holy grail' of exoplanet research today is the detection of an earth-like planet: a rocky planet in the habitable zone around a main-sequence star. Extremely precise Doppler spectroscopy is an indispensable tool to find and characterize earth-like planets; however, to find these planets around solar-type stars, we need nearly one order of magnitude better radial velocity (RV) precision than the best current spectrographs provide. Recent developments in astrophotonics (Bland-Hawthorn & Horton 2006, Bland-Hawthorn et al. 2010) and adaptive optics (AO) enable single mode fiber (SMF) fed, high resolution spectrographs, which can realize the next step in precision. SMF feeds have intrinsic advantages over multimode fiber or slit coupled spectrographs: The intensity distribution at the fiber exit is extremely stable, and as a result the line spread function of a well-designed spectrograph is fully decoupled from input coupling conditions, like guiding or seeing variations (Ihle et al. 2010). Modal noise, a limiting factor in current multimode fiber fed instruments (Baudrand & Walker 2001), can be eliminated by proper design, and the diffraction limited input to the spectrograph allows for very compact instrument designs, which provide excellent optomechanical stability. A SMF is the ideal interface for new, very precise wavelength calibrators, like laser frequency combs (Steinmetz et al. 2008, Osterman et al. 2012), or SMF based Fabry-Perot Etalons (Halverson et al. 2013). At near infrared wavelengths, these technologies are ready to be implemented in on-sky instruments, or already in use. We discuss a novel concept for such a spectrograph.

Function-based classification of carbohydrate-active enzymes by recognition of short, conserved peptide motifs.

PubMed

Busk, Peter Kamp; Lange, Lene

2013-06-01

Functional prediction of carbohydrate-active enzymes is difficult due to low sequence identity. However, similar enzymes often share a few short motifs, e.g., around the active site, even when the overall sequences are very different. To exploit this notion for functional prediction of carbohydrate-active enzymes, we developed a simple algorithm, peptide pattern recognition (PPR), that can divide proteins into groups of sequences that share a set of short conserved sequences. When this method was used on 118 glycoside hydrolase 5 proteins with 9% average pairwise identity and representing four characterized enzymatic functions, 97% of the proteins were sorted into groups correlating with their enzymatic activity. Furthermore, we analyzed 8,138 glycoside hydrolase 13 proteins including 204 experimentally characterized enzymes with 28 different functions. There was a 91% correlation between group and enzyme activity. These results indicate that the function of carbohydrate-active enzymes can be predicted with high precision by finding short, conserved motifs in their sequences. The glycoside hydrolase 61 family is important for fungal biomass conversion, but only a few proteins of this family have been functionally characterized. Interestingly, PPR divided 743 glycoside hydrolase 61 proteins into 16 subfamilies useful for targeted investigation of the function of these proteins and pinpointed three conserved motifs with putative importance for enzyme activity. Furthermore, the conserved sequences were useful for cloning of new, subfamily-specific glycoside hydrolase 61 proteins from 14 fungi. In conclusion, identification of conserved sequence motifs is a new approach to sequence analysis that can predict carbohydrate-active enzyme functions with high precision.

Centromere reference models for human chromosomes X and Y satellite arrays

PubMed Central

Miga, Karen H.; Newton, Yulia; Jain, Miten; Altemose, Nicolas; Willard, Huntington F.; Kent, W. James

2014-01-01

The human genome sequence remains incomplete, with multimegabase-sized gaps representing the endogenous centromeres and other heterochromatic regions. Available sequence-based studies within these sites in the genome have demonstrated a role in centromere function and chromosome pairing, necessary to ensure proper chromosome segregation during cell division. A common genomic feature of these regions is the enrichment of long arrays of near-identical tandem repeats, known as satellite DNAs, which offer a limited number of variant sites to differentiate individual repeat copies across millions of bases. This substantial sequence homogeneity challenges available assembly strategies and, as a result, centromeric regions are omitted from ongoing genomic studies. To address this problem, we utilize monomer sequence and ordering information obtained from whole-genome shotgun reads to model two haploid human satellite arrays on chromosomes X and Y, resulting in an initial characterization of 3.83 Mb of centromeric DNA within an individual genome. To further expand the utility of each centromeric reference sequence model, we evaluate sites within the arrays for short-read mappability and chromosome specificity. Because satellite DNAs evolve in a concerted manner, we use these centromeric assemblies to assess the extent of sequence variation among 366 individuals from distinct human populations. We thus identify two satellite array variants in both X and Y centromeres, as determined by array length and sequence composition. This study provides an initial sequence characterization of a regional centromere and establishes a foundation to extend genomic characterization to these sites as well as to other repeat-rich regions within complex genomes. PMID:24501022

The Isolation of Invertase from Baker's Yeast: A Four-Part Exercise in Protein Purification and Characterization

ERIC Educational Resources Information Center

Timerman, Anthony P.; Fenrick, Angela M.; Zamis, Thomas M.

2009-01-01

A sequence of exercises for the isolation and characterization of invertase (E.C. 3.1.2.26) from baker's yeast obtained from a local grocery store is outlined. Because the enzyme is colorless, the use of colored markers and the sequence of purification steps are designed to "visualize" the process by which a colorless protein is selectively…

Evaluating Community Readiness to Implement Environmental and Policy-Based Alcohol Abuse Prevention Strategies in Wisconsin

ERIC Educational Resources Information Center

Paltzer, Jason; Black, Penny; Moberg, D. Paul

2013-01-01

Background: Matching evidence-based alcohol prevention strat- egies with a community's readiness to support those strategies is the basis for the Tri-Ethnic Community Readiness Model (CRM). The purpose of this evaluation was to assess the association of a community's readiness to address alcohol abuse in their community with the implementation of…

The Kindergarten Academic and Behavior Readiness Screener: The Utility of Single-Item Teacher Ratings of Kindergarten Readiness

ERIC Educational Resources Information Center

Stormont, Melissa; Herman, Keith C.; Reinke, Wendy M.; King, Kathleen R.; Owens, Sarah

2015-01-01

The purpose of the study was to explore the effectiveness of a brief, feasible, and cost-effective universal screener for kindergarten readiness. The study examined whether teacher ratings of kindergarteners' academic, behavioral, and overall readiness at the beginning of the year were predictive of academic, emotional, and behavioral outcomes at…

Empirically-Derived, Person-Oriented Patterns of School Readiness in Typically-Developing Children: Description and Prediction to First-Grade Achievement

ERIC Educational Resources Information Center

Konold, Timothy R.; Pianta, Robert C.

2005-01-01

School readiness assessment is a prominent feature of early childhood education. Because the construct of readiness is multifaceted, we examined children's patterns on multiple indicators previously found to be both theoretically and empirically linked to school readiness: social skill, interactions with parents, problem behavior, and performance…

45 CFR 286.105 - What limitations concerning vocational education, job search and job readiness assistance exist...

Code of Federal Regulations, 2013 CFR

2013-10-01

..., job search and job readiness assistance exist with respect to the work participation rate? 286.105... vocational education, job search and job readiness assistance exist with respect to the work participation... 12 months. (b) There are two limitations concerning job search and job readiness: (1) Job search and...

Pathways to School Readiness: Executive Functioning Predicts Academic and Social-Emotional Aspects of School Readiness

ERIC Educational Resources Information Center

Mann, Trisha D.; Hund, Alycia M.; Hesson-McInnis, Matthew S.; Roman, Zachary J.

2017-01-01

The current study specified the extent to which hot and cool aspects of executive functioning predicted academic and social-emotional indicators of school readiness. It was unique in focusing on positive aspects of social-emotional readiness, rather than problem behaviors. One hundred four 3-5-year-old children completed tasks measuring executive…

Validity of the Bracken School Readiness Assessment for Predicting First Grade Readiness

ERIC Educational Resources Information Center

Panter, Janet E.; Bracken, Bruce A.

2009-01-01

The Bracken School Readiness Assessment (BSRA) was administered to all kindergarten students enrolled in two rural elementary schools in the fall of 2004. Eight months later, the reading portion of the Metropolitan Readiness Tests, 6th Edition (MRT-6) was administered. Teachers were asked to indicate whether they had concerns about each student's…

What It Takes To Support School Readiness: Building Collaborative Partnerships. Program Services Paper.

ERIC Educational Resources Information Center

Brown, Glyn

This guide is intended to help collaborative groups work together more effectively to promote children's readiness for school and provides useful information on the many factors that affect school readiness. The guide notes North Carolina's definition of school readiness as the condition of children as they enter school, based on five…

Work Readiness Standards and Benchmarks: The Key to Differentiating America's Workforce and Regaining Global Competitiveness

ERIC Educational Resources Information Center

Clark, Hope

2013-01-01

In this report, ACT presents a definition of "work readiness" along with empirically driven ACT Work Readiness Standards and Benchmarks. The introduction of standards and benchmarks for workplace success provides a more complete picture of the factors that are important in establishing readiness for success throughout a lifetime. While…

Ready, Steady, Learn: School Readiness and Children's Voices in English Early Childhood Settings

ERIC Educational Resources Information Center

Brooks, Elspeth; Murray, Jane

2018-01-01

Internationally, school readiness is increasingly the rationale for early childhood education and care (ECEC). This is the case in England, yet the statutory English Early Years Foundation Stage framework for children 0-5 years also requires practitioners to listen to children's voices: discourse indicates dissonance between school readiness and…

"Por Los Ojos De Madres": Latina Mothers' Understandings of College Readiness

ERIC Educational Resources Information Center

Cortez, Laura Jean; Martinez, Melissa Ann; Sáenz, Victor B.

2014-01-01

In this study, data from six focus groups with 30 Latina mothers in South Texas were analyzed utilizing a "funds of knowledge" approach to uncover their understandings of college readiness and their role in ensuring their children are college ready. Findings indicate that Latina mothers perceived college readiness in a holistic fashion,…

78 FR 63454 - Meeting of the Department of Defense Military Family Readiness Council (MFRC); Cancellation of...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-24

... Readiness Council (MFRC); Cancellation of October 18, 2013 Meeting AGENCY: Department of Defense. ACTION... Readiness Council (MFRC) that was to take place on Friday, October 18, 2013. The meeting of October 18, 2013... of the Department of Defense Military Family Readiness Council on October 18, 2013. As a result, the...

The Federal Nursing Service Award. Individual readiness in nursing.

PubMed

Reineck, C

1999-04-01

Individual readiness is critical for effective nursing in deployed environments. Although readiness is routinely tracked and reported, a study of its complexity among federal nurses was needed. An inductive research approach clarified the concept of individual readiness. Representing a broad range of deployment experience, focus group members developed a definition of the concept and identified six components: clinical competency; operational competency; survival skills; personal/psychosocial/physical readiness; leadership and administrative support; and group integration and identification. The findings form an overdue conceptual basis for future measurement of this important dimension of federal nursing.

Readiness factors for information system strategic planning among universities in developing countries: a systematic review

NASA Astrophysics Data System (ADS)

Irfan, M.; Putra, S. J.; Alam, C. N.; Subiyakto, A.; Wahana, A.

2018-03-01

The implementation of information system strategic planning (ISSP) in higher education institutions is to improve work efficiency, management effectiveness in order to improve organizational competitive advantage. However, the question of whether all universities are ready to implement ISSP as a way to achieve organizational goals has not been answered. This study aims to investigate the readiness phenomena through literature study. The method used is by using the Systematic Literature Review (SLR) instrument to identify readiness factors on the implementation of ISSP, especially among the institutions of higher education in developing countries. This study has identified 10 readiness measurement. There are three categories of measurement, namely people, processes and technologies that represent 11 factors of ISSP readiness measurement in universities.

Social Information Processing Patterns, Social Skills, and School Readiness in Preschool Children

PubMed Central

Ziv, Yair

2012-01-01

The links between social information processing, social competence, and school readiness were examined in this short-term longitudinal study with a sample of 198 preschool children. Data on social information processing were obtained via child interview, data on child social competence were obtained via teacher report, and data on school readiness were obtained via child assessment (early literacy skills) and teacher report (approaches to learning). Findings provided support for our hypothesis that both social information processing and social competence are related to school readiness. Social competence also partially mediated the link between social information processing and school readiness thus supporting our hypothesis about an indirect path in which mental processes are translated into social skills and then translated into school readiness. PMID:23046690

LWRS ATR Irradiation Testing Readiness Status

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

Kristine Barrett

2012-09-01

The Light Water Reactor Sustainability (LWRS) Program was established by the U.S. Department of Energy Office of Nuclear Energy (DOE-NE) to develop technologies and other solutions that can improve the reliability, sustain the safety, and extend the life of the current reactors. The LWRS Program is divided into four R&D Pathways: (1) Materials Aging and Degradation; (2) Advanced Light Water Reactor Nuclear Fuels; (3) Advanced Instrumentation, Information and Control Systems; and (4) Risk-Informed Safety Margin Characterization. This report describes an irradiation testing readiness analysis in preparation of LWRS experiments for irradiation testing at the Idaho National Laboratory (INL) Advanced Testmore » Reactor (ATR) under Pathway (2). The focus of the Advanced LWR Nuclear Fuels Pathway is to improve the scientific knowledge basis for understanding and predicting fundamental performance of advanced nuclear fuel and cladding in nuclear power plants during both nominal and off-nominal conditions. This information will be applied in the design and development of high-performance, high burn-up fuels with improved safety, cladding integrity, and improved nuclear fuel cycle economics« less

The (in)complete organelle genome: exploring the use and nonuse of available technologies for characterizing mitochondrial and plastid chromosomes.

PubMed

Sanitá Lima, Matheus; Woods, Laura C; Cartwright, Matthew W; Smith, David Roy

2016-11-01

Not long ago, scientists paid dearly in time, money and skill for every nucleotide that they sequenced. Today, DNA sequencing technologies epitomize the slogan 'faster, easier, cheaper and more', and in many ways, sequencing an entire genome has become routine, even for the smallest laboratory groups. This is especially true for mitochondrial and plastid genomes. Given their relatively small sizes and high copy numbers per cell, organelle DNAs are currently among the most highly sequenced kind of chromosome. But accurately characterizing an organelle genome and the information it encodes can require much more than DNA sequencing and bioinformatics analyses. Organelle genomes can be surprisingly complex and can exhibit convoluted and unconventional modes of gene expression. Unravelling this complexity can demand a wide assortment of experiments, from pulsed-field gel electrophoresis to Southern and Northern blots to RNA analyses. Here, we show that it is exactly these types of 'complementary' analyses that are often lacking from contemporary organelle genome papers, particularly short 'genome announcement' articles. Consequently, crucial and interesting features of organelle chromosomes are going undescribed, which could ultimately lead to a poor understanding and even a misrepresentation of these genomes and the genes they express. High-throughput sequencing and bioinformatics have made it easy to sequence and assemble entire chromosomes, but they should not be used as a substitute for or at the expense of other types of genomic characterization methods. © 2016 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

3' terminal diversity of MRP RNA and other human noncoding RNAs revealed by deep sequencing.

PubMed

Goldfarb, Katherine C; Cech, Thomas R

2013-09-21

Post-transcriptional 3' end processing is a key component of RNA regulation. The abundant and essential RNA subunit of RNase MRP has been proposed to function in three distinct cellular compartments and therefore may utilize this mode of regulation. Here we employ 3' RACE coupled with high-throughput sequencing to characterize the 3' terminal sequences of human MRP RNA and other noncoding RNAs that form RNP complexes. The 3' terminal sequence of MRP RNA from HEK293T cells has a distinctive distribution of genomically encoded termini (including an assortment of U residues) with a portion of these selectively tagged by oligo(A) tails. This profile contrasts with the relatively homogenous 3' terminus of an in vitro transcribed MRP RNA control and the differing 3' terminal profiles of U3 snoRNA, RNase P RNA, and telomerase RNA (hTR). 3' RACE coupled with deep sequencing provides a valuable framework for the functional characterization of 3' terminal sequences of noncoding RNAs.

[Morphological and molecular characterization of isolates of Macrophomina phaseolina associated with sugarcane in Mexico].

PubMed

Leyva-Mir, Santos G; Velázquez-Martínez, Guadalupe C; Tlapal-Bolaños, Bertha; Tovar-Pedraza, Juan M; Rosas-Saito, Greta H; Alvarado-Gómez, Omar G

2015-01-01

Charcoal rot caused by Macrophomina phaseolina is an important disease of sugarcane in Mexico. This study was carried out to characterize isolates of M. phaseolina obtained from sugarcane by the combination of morphological and molecular analyses. The morphological characterization of 10 isolates was performed using scanning electron microscopy and light microscopy. To confirm the morphological identification, rDNA from two representative isolates was extracted, and the internal transcribed spacer (ITS) region was amplified by polymerase chain reaction and sequenced using specific primers MpKF1 and MpKR1. Based on their morphological characteristics, all isolates were identified as M. phaseolina. Moreover, the analysis of two ITS sequences showed 100% similarity with the M. phaseolina sequences deposited in the GenBank. To our knowledge, this is the first study in the world aimed at characterizing isolates of M. phaseolina obtained from sugarcane. Copyright © 2014 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

Floral gene resources from basal angiosperms for comparative genomics research

PubMed Central

Albert, Victor A; Soltis, Douglas E; Carlson, John E; Farmerie, William G; Wall, P Kerr; Ilut, Daniel C; Solow, Teri M; Mueller, Lukas A; Landherr, Lena L; Hu, Yi; Buzgo, Matyas; Kim, Sangtae; Yoo, Mi-Jeong; Frohlich, Michael W; Perl-Treves, Rafael; Schlarbaum, Scott E; Bliss, Barbara J; Zhang, Xiaohong; Tanksley, Steven D; Oppenheimer, David G; Soltis, Pamela S; Ma, Hong; dePamphilis, Claude W; Leebens-Mack, James H

2005-01-01

Background The Floral Genome Project was initiated to bridge the genomic gap between the most broadly studied plant model systems. Arabidopsis and rice, although now completely sequenced and under intensive comparative genomic investigation, are separated by at least 125 million years of evolutionary time, and cannot in isolation provide a comprehensive perspective on structural and functional aspects of flowering plant genome dynamics. Here we discuss new genomic resources available to the scientific community, comprising cDNA libraries and Expressed Sequence Tag (EST) sequences for a suite of phylogenetically basal angiosperms specifically selected to bridge the evolutionary gaps between model plants and provide insights into gene content and genome structure in the earliest flowering plants. Results Random sequencing of cDNAs from representatives of phylogenetically important eudicot, non-grass monocot, and gymnosperm lineages has so far (as of 12/1/04) generated 70,514 ESTs and 48,170 assembled unigenes. Efficient sorting of EST sequences into putative gene families based on whole Arabidopsis/rice proteome comparison has permitted ready identification of cDNA clones for finished sequencing. Preliminarily, (i) proportions of functional categories among sequenced floral genes seem representative of the entire Arabidopsis transcriptome, (ii) many known floral gene homologues have been captured, and (iii) phylogenetic analyses of ESTs are providing new insights into the process of gene family evolution in relation to the origin and diversification of the angiosperms. Conclusion Initial comparisons illustrate the utility of the EST data sets toward discovery of the basic floral transcriptome. These first findings also afford the opportunity to address a number of conspicuous evolutionary genomic questions, including reproductive organ transcriptome overlap between angiosperms and gymnosperms, genome-wide duplication history, lineage-specific gene duplication and functional divergence, and analyses of adaptive molecular evolution. Since not all genes in the floral transcriptome will be associated with flowering, these EST resources will also be of interest to plant scientists working on other functions, such as photosynthesis, signal transduction, and metabolic pathways. PMID:15799777

Sequence analysis of a few species of termites (Order: Isoptera) on the basis of partial characterization of COII gene.

PubMed

Sobti, Ranbir Chander; Kumari, Mamtesh; Sharma, Vijay Lakshmi; Sodhi, Monika; Mukesh, Manishi; Shouche, Yogesh

2009-11-01

The present study was aimed to get the nucleotide sequences of a part of COII mitochondrial gene amplified from individuals of five species of Termites (Isoptera: Termitidae: Macrotermitinae). Four of them belonged to the genus Odontotermes (O. obesus, O. horni, O. bhagwatii and Odontotermes sp.) and one to Microtermes (M. obesi). Partial COII gene fragments were amplified by using specific primers. The sequences so obtained were characterized to calculate the frequencies of each nucleotide bases and a high A + T content was observed. The interspecific pairwise sequence divergence in Odontotermes species ranged from 6.5% to 17.1% across COII fragment. M. obesi sequence diversity ranged from 2.5 with Odontotermes sp. to 19.0% with O. bhagwatii. Phylogenetic trees drawn on the basis of distance neighbour-joining method revealed three main clades clustering all the individuals according to their genera and families.

Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.

PubMed

Mayer, K; Schüller, C; Wambutt, R; Murphy, G; Volckaert, G; Pohl, T; Düsterhöft, A; Stiekema, W; Entian, K D; Terryn, N; Harris, B; Ansorge, W; Brandt, P; Grivell, L; Rieger, M; Weichselgartner, M; de Simone, V; Obermaier, B; Mache, R; Müller, M; Kreis, M; Delseny, M; Puigdomenech, P; Watson, M; Schmidtheini, T; Reichert, B; Portatelle, D; Perez-Alonso, M; Boutry, M; Bancroft, I; Vos, P; Hoheisel, J; Zimmermann, W; Wedler, H; Ridley, P; Langham, S A; McCullagh, B; Bilham, L; Robben, J; Van der Schueren, J; Grymonprez, B; Chuang, Y J; Vandenbussche, F; Braeken, M; Weltjens, I; Voet, M; Bastiaens, I; Aert, R; Defoor, E; Weitzenegger, T; Bothe, G; Ramsperger, U; Hilbert, H; Braun, M; Holzer, E; Brandt, A; Peters, S; van Staveren, M; Dirske, W; Mooijman, P; Klein Lankhorst, R; Rose, M; Hauf, J; Kötter, P; Berneiser, S; Hempel, S; Feldpausch, M; Lamberth, S; Van den Daele, H; De Keyser, A; Buysshaert, C; Gielen, J; Villarroel, R; De Clercq, R; Van Montagu, M; Rogers, J; Cronin, A; Quail, M; Bray-Allen, S; Clark, L; Doggett, J; Hall, S; Kay, M; Lennard, N; McLay, K; Mayes, R; Pettett, A; Rajandream, M A; Lyne, M; Benes, V; Rechmann, S; Borkova, D; Blöcker, H; Scharfe, M; Grimm, M; Löhnert, T H; Dose, S; de Haan, M; Maarse, A; Schäfer, M; Müller-Auer, S; Gabel, C; Fuchs, M; Fartmann, B; Granderath, K; Dauner, D; Herzl, A; Neumann, S; Argiriou, A; Vitale, D; Liguori, R; Piravandi, E; Massenet, O; Quigley, F; Clabauld, G; Mündlein, A; Felber, R; Schnabl, S; Hiller, R; Schmidt, W; Lecharny, A; Aubourg, S; Chefdor, F; Cooke, R; Berger, C; Montfort, A; Casacuberta, E; Gibbons, T; Weber, N; Vandenbol, M; Bargues, M; Terol, J; Torres, A; Perez-Perez, A; Purnelle, B; Bent, E; Johnson, S; Tacon, D; Jesse, T; Heijnen, L; Schwarz, S; Scholler, P; Heber, S; Francs, P; Bielke, C; Frishman, D; Haase, D; Lemcke, K; Mewes, H W; Stocker, S; Zaccaria, P; Bevan, M; Wilson, R K; de la Bastide, M; Habermann, K; Parnell, L; Dedhia, N; Gnoj, L; Schutz, K; Huang, E; Spiegel, L; Sehkon, M; Murray, J; Sheet, P; Cordes, M; Abu-Threideh, J; Stoneking, T; Kalicki, J; Graves, T; Harmon, G; Edwards, J; Latreille, P; Courtney, L; Cloud, J; Abbott, A; Scott, K; Johnson, D; Minx, P; Bentley, D; Fulton, B; Miller, N; Greco, T; Kemp, K; Kramer, J; Fulton, L; Mardis, E; Dante, M; Pepin, K; Hillier, L; Nelson, J; Spieth, J; Ryan, E; Andrews, S; Geisel, C; Layman, D; Du, H; Ali, J; Berghoff, A; Jones, K; Drone, K; Cotton, M; Joshu, C; Antonoiu, B; Zidanic, M; Strong, C; Sun, H; Lamar, B; Yordan, C; Ma, P; Zhong, J; Preston, R; Vil, D; Shekher, M; Matero, A; Shah, R; Swaby, I K; O'Shaughnessy, A; Rodriguez, M; Hoffmann, J; Till, S; Granat, S; Shohdy, N; Hasegawa, A; Hameed, A; Lodhi, M; Johnson, A; Chen, E; Marra, M; Martienssen, R; McCombie, W R

1999-12-16

The higher plant Arabidopsis thaliana (Arabidopsis) is an important model for identifying plant genes and determining their function. To assist biological investigations and to define chromosome structure, a coordinated effort to sequence the Arabidopsis genome was initiated in late 1996. Here we report one of the first milestones of this project, the sequence of chromosome 4. Analysis of 17.38 megabases of unique sequence, representing about 17% of the genome, reveals 3,744 protein coding genes, 81 transfer RNAs and numerous repeat elements. Heterochromatic regions surrounding the putative centromere, which has not yet been completely sequenced, are characterized by an increased frequency of a variety of repeats, new repeats, reduced recombination, lowered gene density and lowered gene expression. Roughly 60% of the predicted protein-coding genes have been functionally characterized on the basis of their homology to known genes. Many genes encode predicted proteins that are homologous to human and Caenorhabditis elegans proteins.

Assessing infant and maternal readiness for newborn discharge.

PubMed

Jing, Ling; Bethancourt, Casidhe-Nicole; McDonagh, Thomas

2017-10-01

The review highlights the shift from prescribed length of stay (LOS) to mother-infant dyad readiness as the basis for making discharge decisions for healthy term newborns. We describe the components of readiness that should be considered in making the decision, focusing on infant clinical readiness, and maternal and familial readiness. Although the Newborns' and Mothers' Health Protection Act of 1996 aimed to protect infants and mothers by establishing a minimum LOS, the American Academy of Pediatrics 2015 policy on newborn discharge acknowledges the shift from LOS-based to readiness-based discharge decision-making. Healthcare providers must consider a variety of infant and maternal characteristics in determining the appropriate time to discharge a dyad, and mothers should be actively involved in the decision-making process. Criteria for infant clinical readiness include the following: establishment of effective feeding, evaluation of jaundice risk, review and discussion of infant and household vaccination status, obtainment of specimen for metabolic screening, tests of hearing ability, assessment of sepsis risk factors, screening for congenital heart disease, and evaluation of parental knowledge about infant safety measures. Important consideration should also be given to the mother's sociodemographic vulnerabilities, maternal confidence and perception of discharge readiness, and availability of postdischarge care continuity. The timing of newborn discharge should be a joint decision made by the mother and healthcare providers based on readiness. The decision should consider the infant's health status, the mother's health status, the mother's perception of readiness, and the availability of social and familial support for the mother and infant. Accessible and comprehensive support postdischarge is also important for helping infants achieve optimal health outcomes.

Mixed Picture of Readiness for Adoption of Evidence-Based Prevention Programs in Communities: Exploratory Surveys of State Program Delivery Systems

PubMed Central

Schainker, Lisa M.; Redmond, Cleve; Ralston, Ekaterina; Yeh, Hsiu-Chen; Perkins, Daniel F.

2015-01-01

An emerging literature highlights the potential for broader dissemination of evidence-based prevention programs in communities through existing state systems, such as the land grant university Extension outreach system and departments of public education and health (DOE– DPH). This exploratory study entailed surveying representatives of the national Extension system and DOE– DPH, to evaluate dissemination readiness factors, as part of a larger project on an evidence-based program delivery model called PROSPER. In addition to assessing systems’ readiness factors, differences among US regions and comparative levels of readiness between state systems were evaluated. The Extension web-based survey sample N was 958 and the DOE–DPH telephone survey N was 338, with response rates of 23 and 79 %, respectively. Extension survey results suggested only a moderate level of overall readiness nationally, with relatively higher perceived need for collaborative efforts and relatively lower perceived resource availability. There were significant regional differences on all factors, generally favoring the Northeast. Results from DOE–DPH surveys showed significantly higher levels for all readiness factors, compared with Extension systems. Overall, the findings present a mixed picture. Although there were clear challenges related to measuring readiness in complex systems, addressing currently limited dissemination resources, and devising strategies for optimizing readiness, all systems showed some readiness-related strengths. PMID:25791916

The psychometric properties of the Readiness and Motivation Questionnaire: a symptom-specific measure of readiness for change in the eating disorders.

PubMed

Geller, Josie; Brown, Krista E; Srikameswaran, Suja; Piper, William; Dunn, Erin C

2013-09-01

Readiness for change, as assessed by the readiness and motivation interview (RMI), predicts a number of clinical outcome variables in eating disorders including enrollment in intensive treatment, symptom change, dropout, and relapse. Although clinically useful, the training and administration of the RMI is time consuming. The purpose of this research was to (a) develop a self-report, symptom-specific version of the RMI, the readiness and motivation questionnaire (RMQ), that can be used to assess readiness for change across all eating disorder diagnoses and (b) establish its psychometric properties. The RMQ provides stage of change, internality, and confidence scores for each of 4 eating disorder symptom domains (restriction, bingeing, and cognitive and compensatory behaviors). Individuals (N = 244) with current eating disorder diagnoses completed the RMQ and measures of convergent, discriminant, and criterion validity. Similar to the RMI scores, readiness scores on the RMQ differed according to symptom domain. Regarding criterion validity, RMQ scores were significantly associated with ratings of anticipated difficulty of recovery activities and completion of recovery activities. The RMQ contributed significant unique variance to anticipated difficulty of recovery activities, beyond those accounted for by the RMI and a questionnaire measure of global readiness. The RMQ is thus an acceptable alternative to the RMI, providing global and domain-specific readiness information when time or cost prohibits use of an interview.

Human papillomavirus type 18 variant lineages in United States populations characterized by sequence analysis of LCR-E6, E2, and L1 regions.

PubMed

Arias-Pulido, Hugo; Peyton, Cheri L; Torrez-Martínez, Norah; Anderson, D Nelson; Wheeler, Cosette M

2005-07-20

While HPV 16 variant lineages have been well characterized, the knowledge about HPV 18 variants is limited. In this study, HPV 18 nucleotide variations in the E2 hinge region were characterized by sequence analysis in 47 control and 51 tumor specimens. Fifty of these specimens were randomly selected for sequencing of an LCR-E6 segment and 20 samples representative of LCR-E6 and E2 sequence variants were examined across the L1 region. A total of 2770 nucleotides per HPV 18 variant genome were considered in this study. HPV 18 variant nucleotides were linked among all gene segments analyzed and grouped into three main branches: Asian-American (AA), European (E), and African (Af). These three branches were equally distributed among controls and cases and when stratified by Hispanic and non-Hispanic ethnicities. Among invasive cervical cancer cases, no significant differences in the three HPV variant branches were observed among ethnic groups or when stratified by histopathology (squamous vs. adenocarcinoma). The Af branch showed the greatest nucleotide variability when compared to the HPV 18 reference sequence and was more closely related to HPV 45 than either AA or E branches. Our data also characterize nucleotide and amino acid variations in the L1 capsid gene among HPV 18 variants, which may be relevant to vaccine strategies and subsequent studies of naturally occurring HPV 18 variants. Several novel HPV 18 nucleotide variations were identified in this study.

Serotype IV Sequence Type 468 Group B Streptococcus Neonatal Invasive Disease, Minnesota, USA.

PubMed

Teatero, Sarah; Ferrieri, Patricia; Fittipaldi, Nahuel

2016-11-01

To further understand the emergence of serotype IV group B Streptococcus (GBS) invasive disease, we used whole-genome sequencing to characterize 3 sequence type 468 strains isolated from neonates in Minnesota, USA. We found that strains of tetracycline-resistant sequence type 468 GBS have acquired virulence genes from a putative clonal complex 17 GBS donor by recombination.

Bacterial diversity in permanently cold and alkaline ikaite columns from Greenland.

PubMed

Schmidt, Mariane; Priemé, Anders; Stougaard, Peter

2006-12-01

Bacterial diversity in alkaline (pH 10.4) and permanently cold (4 degrees C) ikaite tufa columns from the Ikka Fjord, SW Greenland, was investigated using growth characterization of cultured bacterial isolates with Terminal-restriction fragment length polymorphism (T-RFLP) and sequence analysis of bacterial 16S rRNA gene fragments. More than 200 bacterial isolates were characterized with respect to pH and temperature tolerance, and it was shown that the majority were cold-active alkaliphiles. T-RFLP analysis revealed distinct bacterial communities in different fractions of three ikaite columns, and, along with sequence analysis, it showed the presence of rich and diverse bacterial communities. Rarefaction analysis showed that the 109 sequenced clones in the 16S rRNA gene library represented between 25 and 65% of the predicted species richness in the three ikaite columns investigated. Phylogenetic analysis of the 16S rRNA gene sequences revealed many sequences with similarity to alkaliphilic or psychrophilic bacteria, and showed that 33% of the cloned sequences and 33% of the cultured bacteria showed less than 97% sequence identity to known sequences in databases, and may therefore represent yet unknown species.

Making It Real: How High Schools Can Be Held Accountable for Developing Students' Career Readiness. Policy Brief 13-2

ERIC Educational Resources Information Center

Darche, Svetlana; Stern, David

2013-01-01

There is widespread agreement on the goal of preparing every high school student for both postsecondary education and a lifetime of fulfilling work, that every graduate should be "college and career ready." The authors' view is that career readiness and college readiness entail many of the same skills, bodies of knowledge, and…

Assessment of the Florida College and Career Readiness Initiative: Year 2 Report, Executive Summary

ERIC Educational Resources Information Center

Mokher, Christine; Jacobson, Lou

2014-01-01

The Florida College and Career Readiness Initiative (FCCRI) is a statewide program designed to assess the college readiness of high school students in 11th grade, and for those assessed as not college-ready, to provide instruction in the 12th grade that will lead to their college success. The assessment used is the Postsecondary Education…

Measuring Success: David Conley's College Readiness Framework and the Illinois College and Career Readiness Act. In Brief

ERIC Educational Resources Information Center

Baber, Lorenzo D.; Castro, Erin L.; Bragg, Debra D.

2010-01-01

The purpose of this brief is to understand the Illinois College and Career Readiness (CCR) Act in light of David Conley's college readiness model. Although not mentioned specifically by the Illinois statute, evaluation results gathered by the Office of Community College Research and Leadership (OCCRL) show alignment between a number of programs…