Motion and Energy Chemical Reactions, Parts One & Two of an Integrated Science Sequence, Student Guide, 1971 Edition.

ERIC Educational Resources Information Center

Portland Project Committee, OR.

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

A planning and scheduling lexicon

NASA Technical Reports Server (NTRS)

Cruz, Jennifer W.; Eggemeyer, William C.

1989-01-01

A lexicon related to mission planning and scheduling for spacecraft is presented. Planning and scheduling work is known as sequencing. Sequencing is a multistage process of merging requests from both the science and engineering arenas to accomplish the objectives defined in the requests. The multistage process begins with the creation of science and engineering goals, continues through their integration into the sequence, and eventually concludes with command execution onboard the spacecraft. The objective of this publication is to introduce some formalism into the field of spacecraft sequencing-system technology. This formalism will make it possible for researchers and potential customers to communicate about system requirements and capabilities in a common language.

The Human Genome Project: big science transforms biology and medicine

PubMed Central

2013-01-01

The Human Genome Project has transformed biology through its integrated big science approach to deciphering a reference human genome sequence along with the complete sequences of key model organisms. The project exemplifies the power, necessity and success of large, integrated, cross-disciplinary efforts - so-called ‘big science’ - directed towards complex major objectives. In this article, we discuss the ways in which this ambitious endeavor led to the development of novel technologies and analytical tools, and how it brought the expertise of engineers, computer scientists and mathematicians together with biologists. It established an open approach to data sharing and open-source software, thereby making the data resulting from the project accessible to all. The genome sequences of microbes, plants and animals have revolutionized many fields of science, including microbiology, virology, infectious disease and plant biology. Moreover, deeper knowledge of human sequence variation has begun to alter the practice of medicine. The Human Genome Project has inspired subsequent large-scale data acquisition initiatives such as the International HapMap Project, 1000 Genomes, and The Cancer Genome Atlas, as well as the recently announced Human Brain Project and the emerging Human Proteome Project. PMID:24040834

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

ERIC Educational Resources Information Center

Portland Project Committee, OR.

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

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

ERIC Educational Resources Information Center

Bixby, Louis W.; And Others

Material for the first year of Energy/Structure/Life, a two-year high school program in integrated science, is contained in this learning guide. The program, a sequence of physics, chemistry, and biology, presents the physical science phase during the first year with these 13 chapters: (1) distance/time/velocity; (2) velocity/change/acceleration;…

Accelerated Integrated Science Sequence: Interdisciplinary Undergraduate Science for the 21st Century

ERIC Educational Resources Information Center

Ulsh, Lisa S.

2011-01-01

Numerous reports cite the need to improve the quality of undergraduate STEM education in order to attract and train a diverse pool of talented students prepared to meet the scientific and technological challenges of the 21st century. A growing body of research reveals that the nature and quality of science instruction in introductory college…

Decision Making Associated with Selecting an Integrated or a Discipline Model for Middle School Science Instruction

ERIC Educational Resources Information Center

Brockbank, Brennan R.

2017-01-01

Purpose: This study sought to identify, understand, and describe the decision-making processes used by school districts to determine the middle school science course sequence as part of the adoption of the Next Generation Science Standards. Additionally, this study explored and described the expressed comments, feelings, and beliefs of…

Introductory Life Science Mathematics and Quantitative Neuroscience Courses

ERIC Educational Resources Information Center

Duffus, Dwight; Olifer, Andrei

2010-01-01

We describe two sets of courses designed to enhance the mathematical, statistical, and computational training of life science undergraduates at Emory College. The first course is an introductory sequence in differential and integral calculus, modeling with differential equations, probability, and inferential statistics. The second is an…

Sequencing Data Discovery and Integration for Earth System Science with MetaSeek

NASA Astrophysics Data System (ADS)

Hoarfrost, A.; Brown, N.; Arnosti, C.

2017-12-01

Microbial communities play a central role in biogeochemical cycles. Sequencing data resources from environmental sources have grown exponentially in recent years, and represent a singular opportunity to investigate microbial interactions with Earth system processes. Carrying out such meta-analyses depends on our ability to discover and curate sequencing data into large-scale integrated datasets. However, such integration efforts are currently challenging and time-consuming, with sequencing data scattered across multiple repositories and metadata that is not easily or comprehensively searchable. MetaSeek is a sequencing data discovery tool that integrates sequencing metadata from all the major data repositories, allowing the user to search and filter on datasets in a lightweight application with an intuitive, easy-to-use web-based interface. Users can save and share curated datasets, while other users can browse these data integrations or use them as a jumping off point for their own curation. Missing and/or erroneous metadata are inferred automatically where possible, and where not possible, users are prompted to contribute to the improvement of the sequencing metadata pool by correcting and amending metadata errors. Once an integrated dataset has been curated, users can follow simple instructions to download their raw data and quickly begin their investigations. In addition to the online interface, the MetaSeek database is easily queryable via an open API, further enabling users and facilitating integrations of MetaSeek with other data curation tools. This tool lowers the barriers to curation and integration of environmental sequencing data, clearing the path forward to illuminating the ecosystem-scale interactions between biological and abiotic processes.

An integrated semiconductor device enabling non-optical genome sequencing.

PubMed

Rothberg, Jonathan M; Hinz, Wolfgang; Rearick, Todd M; Schultz, Jonathan; Mileski, William; Davey, Mel; Leamon, John H; Johnson, Kim; Milgrew, Mark J; Edwards, Matthew; Hoon, Jeremy; Simons, Jan F; Marran, David; Myers, Jason W; Davidson, John F; Branting, Annika; Nobile, John R; Puc, Bernard P; Light, David; Clark, Travis A; Huber, Martin; Branciforte, Jeffrey T; Stoner, Isaac B; Cawley, Simon E; Lyons, Michael; Fu, Yutao; Homer, Nils; Sedova, Marina; Miao, Xin; Reed, Brian; Sabina, Jeffrey; Feierstein, Erika; Schorn, Michelle; Alanjary, Mohammad; Dimalanta, Eileen; Dressman, Devin; Kasinskas, Rachel; Sokolsky, Tanya; Fidanza, Jacqueline A; Namsaraev, Eugeni; McKernan, Kevin J; Williams, Alan; Roth, G Thomas; Bustillo, James

2011-07-20

The seminal importance of DNA sequencing to the life sciences, biotechnology and medicine has driven the search for more scalable and lower-cost solutions. Here we describe a DNA sequencing technology in which scalable, low-cost semiconductor manufacturing techniques are used to make an integrated circuit able to directly perform non-optical DNA sequencing of genomes. Sequence data are obtained by directly sensing the ions produced by template-directed DNA polymerase synthesis using all-natural nucleotides on this massively parallel semiconductor-sensing device or ion chip. The ion chip contains ion-sensitive, field-effect transistor-based sensors in perfect register with 1.2 million wells, which provide confinement and allow parallel, simultaneous detection of independent sequencing reactions. Use of the most widely used technology for constructing integrated circuits, the complementary metal-oxide semiconductor (CMOS) process, allows for low-cost, large-scale production and scaling of the device to higher densities and larger array sizes. We show the performance of the system by sequencing three bacterial genomes, its robustness and scalability by producing ion chips with up to 10 times as many sensors and sequencing a human genome.

Relay Sequence Generation Software

NASA Technical Reports Server (NTRS)

Gladden, Roy E.; Khanampompan, Teerapat

2009-01-01

Due to thermal and electromagnetic interactivity between the UHF (ultrahigh frequency) radio onboard the Mars Reconnaissance Orbiter (MRO), which performs relay sessions with the Martian landers, and the remainder of the MRO payloads, it is required to integrate and de-conflict relay sessions with the MRO science plan. The MRO relay SASF/PTF (spacecraft activity sequence file/ payload target file) generation software facilitates this process by generating a PTF that is needed to integrate the periods of time during which MRO supports relay activities with the rest of the MRO science plans. The software also generates the needed command products that initiate the relay sessions, some features of which are provided by the lander team, some are managed by MRO internally, and some being derived.

Interdisciplinary research and education at the biology-engineering-computer science interface: a perspective.

PubMed

Tadmor, Brigitta; Tidor, Bruce

2005-09-01

Progress in the life sciences, including genome sequencing and high-throughput experimentation, offers an opportunity for understanding biology and medicine from a systems perspective. This 'new view', which complements the more traditional component-based approach, involves the integration of biological research with approaches from engineering disciplines and computer science. The result is more than a new set of technologies. Rather, it promises a fundamental reconceptualization of the life sciences based on the development of quantitative and predictive models to describe crucial processes. To achieve this change, learning communities are being formed at the interface of the life sciences, engineering and computer science. Through these communities, research and education will be integrated across disciplines and the challenges associated with multidisciplinary team-based science will be addressed.

Math + Science: A Solution. Introductory Investigations. Book 1.

ERIC Educational Resources Information Center

Wiebe, Arthur, Ed.; And Others

Developed for use primarily with middle school age students, this introductory booklet provides a sample of innovative activities that integrate mathematics skills with science processes. The investigations employ a wide variety of readily available and easily understood materials. The 25 activities are sequenced from simple to complex according…

ARISE: American renaissance in science education

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

NONE

1998-09-14

The national standards and state derivatives must be reinforced by models of curricular reform. In this paper, ARISE presents one model based on a set of principles--coherence, integration of the sciences, movement from concrete ideas to abstract ones, inquiry, connection and application, sequencing that is responsive to how people learn.

Spitzer Space Telescope Sequencing Operations Software, Strategies, and Lessons Learned

NASA Technical Reports Server (NTRS)

Bliss, David A.

2006-01-01

The Space Infrared Telescope Facility (SIRTF) was launched in August, 2003, and renamed to the Spitzer Space Telescope in 2004. Two years of observing the universe in the wavelength range from 3 to 180 microns has yielded enormous scientific discoveries. Since this magnificent observatory has a limited lifetime, maximizing science viewing efficiency (ie, maximizing time spent executing activities directly related to science observations) was the key operational objective. The strategy employed for maximizing science viewing efficiency was to optimize spacecraft flexibility, adaptability, and use of observation time. The selected approach involved implementation of a multi-engine sequencing architecture coupled with nondeterministic spacecraft and science execution times. This approach, though effective, added much complexity to uplink operations and sequence development. The Jet Propulsion Laboratory (JPL) manages Spitzer s operations. As part of the uplink process, Spitzer s Mission Sequence Team (MST) was tasked with processing observatory inputs from the Spitzer Science Center (SSC) into efficiently integrated, constraint-checked, and modeled review and command products which accommodated the complexity of non-deterministic spacecraft and science event executions without increasing operations costs. The MST developed processes, scripts, and participated in the adaptation of multi-mission core software to enable rapid processing of complex sequences. The MST was also tasked with developing a Downlink Keyword File (DKF) which could instruct Deep Space Network (DSN) stations on how and when to configure themselves to receive Spitzer science data. As MST and uplink operations developed, important lessons were learned that should be applied to future missions, especially those missions which employ command-intensive operations via a multi-engine sequence architecture.

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

ERIC Educational Resources Information Center

Huheey, James; Sandoval, Amado

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

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

ERIC Educational Resources Information Center

DeVoe, Howard; Hearle, Robert

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

Reading, Writing, and Conducting Inquiry about Science in Kindergarten

ERIC Educational Resources Information Center

Patrick, Helen; Mantzicopoulos, Panayota; Samarapungavan, Ala

2009-01-01

Over the past three years, the authors have worked with kindergarten teachers to develop study units with sequences of integrated science inquiry and literacy activities appropriate for kindergartners. Their work, which is part of the Scientific Literacy Project, has been very successful. The success of the Scientific Literacy Project (SLP) is in…

Integration of Research Into Science-outreach (IRIS): A Video and Web-based Approach

NASA Astrophysics Data System (ADS)

Clay, P. L.; O'Driscoll, B.

2013-12-01

The development of the IRIS (Integration of Research Into Science-outreach) initiative is aimed at using field- and laboratory- based videos and blog entries to enable a sustained outreach relationship between university researchers and local classrooms. IRIS seeks to communicate complex, cutting-edge scientific research in the Earth and Planetary sciences to school-aged children in a simple and interesting manner, in the hope of ameliorating the overall decline of children entering into science and engineering fields in future generations. The primary method of delivery IRIS utilizes is the media of film, ';webinars' and blog entries. Filmed sequences of laboratory work, field work, science demos and mini webinars on current and relevant material in the Earth and Planetary sciences are ';subscribed' to by local schools. Selected sequences are delivered in 20-30 minute film segments with accompanying written material. The level at which the subject matter is currently geared is towards secondary level school-aged children, with the purpose of inspiring and encouraging curiosity, learning and development in scientific research. The video broadcasts are supplemented by a hands-on visit 1-2 times per year by a group of scientists participating in the filmed sequences to the subscribing class, with the objective of engaging and establishing a natural rapport between the class and the scientists that they see in the broadcasts. This transgresses boundaries that traditional 'one off' outreach platforms often aren't able to achieve. The initial results of the IRIS outreach initiative including successes, problems encountered and classroom feedback will be reported.

Integrated Modular Teaching of Human Biology for Primary Care Practitioners

ERIC Educational Resources Information Center

Glasgow, Michael S.

1977-01-01

Describes the use of integrated modular teaching of the human biology component of the Health Associate Program at Johns Hopkins University, where the goal is to develop an understanding of the sciences as applied to primary care. Discussion covers the module sequence, the human biology faculty, goals of the human biology faculty, laboratory…

Accelerated Integrated Science Sequence (AISS): An Introductory Biology, Chemistry, and Physics Course

ERIC Educational Resources Information Center

Purvis-Roberts, Kathleen L.; Edwalds-Gilbert, Gretchen; Landsberg, Adam S.; Copp, Newton; Ulsh, Lisa; Drew, David E.

2009-01-01

A new interdisciplinary, introductory science course was offered for the first time during the 2007-2008 school year. The purpose of the course is to introduce students to the idea of working at the intersections of biology, chemistry, and physics and to recognize interconnections between the disciplines. Interdisciplinary laboratories are a key…

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

ERIC Educational Resources Information Center

Viola, Vic; Hearle, Robert

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

Integrating the New Generation Science Standards (NGSS) into K- 6 teacher training and curricula

NASA Astrophysics Data System (ADS)

Pinter, S.; Carlson, S. J.

2017-12-01

The Next Generation Science Standards is an initiative, adopted by 26 states, to set national education standards that are "rich in content and practice, arranged in a coherent manner across disciplines and grades to provide all students an internationally benchmarked science education." Educators now must integrate these standards into existing curricula. Many grade-school (K-6) teachers face a particularly daunting task, as they were traditionally not required to teach science or only at a rudimentary level. The majority of K-6 teachers enter teaching from non-science disciplines, making this transition even more difficult. Since the NGSS emphasizes integrated and coherent progression of knowledge from grade to grade, prospective K-6 teachers must be able to deliver science with confidence and enthusiasm to their students. CalTeach/MAST (Mathematics and Science Teaching Program) at the University of California Davis, has created a two-quarter sequence of integrated science courses for undergraduate students majoring in non-STEM disciplines and intending to pursue multiple-subject K-6 credentials. The UCD integrated science course provides future primary school teachers with a basic, but comprehensive background in the physical and earth/space sciences. Key tools are taught for improving teaching methods, investigating complex science ideas, and solving problems relevant to students' life experiences that require scientific or technological knowledge. This approach allows prospective K-6 teachers to explore more effectively the connections between the disciplinary core ideas, crosscutting concepts, and scientific and engineering practices, as outlined in the NGSS. In addition, they develop a core set of science teaching skills based on inquiry activities and guided lab discussions. With this course, we deliver a solid science background to prospective K-6 teachers and facilitate their ability to teach science following the standards as articulated in the NGSS.

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

ERIC Educational Resources Information Center

Bixby, Louis W.; And Others

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

Assessing Understanding of Complex Learning Outcomes and Real-World Skills Using an Authentic Software Tool: A Study from Biomedical Sciences

ERIC Educational Resources Information Center

Dermo, John; Boyne, James

2014-01-01

We describe a study conducted during 2009-12 into innovative assessment practice, evaluating an assessed coursework task on a final year Medical Genetics module for Biomedical Science undergraduates. An authentic e-assessment coursework task was developed, integrating objectively marked online questions with an online DNA sequence analysis tool…

Integrating writing into an introductory environmental science curriculum: Perspectives from biology and physics

NASA Astrophysics Data System (ADS)

Selkin, P. A.; Cline, E. T.; Beaufort, A.

2008-12-01

In the University of Washington, Tacoma's Environmental Science program, we are implementing a curriculum-wide, scaffolded strategy to teach scientific writing. Writing in an introductory science course is a powerful means to make students feel part of the scientific community, an important goal in our environmental science curriculum. Writing is already an important component of the UW Tacoma environmental science program at the upper levels: our approach is designed to prepare students for the writing-intensive junior- and senior-level seminars. The approach is currently being tested in introductory biology and physics before it is incorporated in the rest of the introductory environmental science curriculum. The centerpiece of our approach is a set of research and writing assignments woven throughout the biology and physics course sequences. The assignments progress in their degree of complexity and freedom through the sequence of introductory science courses. Each assignment is supported by a number of worksheets and short written exercises designed to teach writing and critical thought skills. The worksheets are focused on skills identified both by research in science writing and the instructors' experience with student writing. Students see the assignments as a way to personalize their understanding of basic science concepts, and to think critically about ideas that interest them. We find that these assignments provide a good way to assess student comprehension of some of the more difficult ideas in the basic sciences, as well as a means to engage students with the challenging concepts of introductory science courses. Our experience designing these courses can inform efforts to integrate writing throughout a geoscience or environmental science curriculum, as opposed to on a course-by-course basis.

Physics First: Impact of course sequencing on the attitudes of female students toward science

NASA Astrophysics Data System (ADS)

O'Connor, Linda Miller

This study was causal-comparative research to determine if there is any relationship between course sequencing and female students' attitudes toward science and their intent to participate in advanced level science courses or pursue science related careers. Physics First promotes the reversal of the traditional sequencing of high school science courses (biology, chemistry and physics) to physics, chemistry and biology or a two or three year integrated European science approach. Physics as a first year high school course of study necessitates changing the course approach to a more conceptual approach and less mathematical and theoretical. Eleventh grade students from two suburban Chicago high schools comprised the sample. The two schools were judged to be extremely similar in their demographic make-up as reported in the 2002 Illinois School Report Card. The notable difference between the schools being the science course sequence recommended for average and above average students. The sample responded to a scanable questionnaire consisting of demographic data and the Test of Science Related Attitudes (TOSRA). TOSRA is a seventy item Likert Scale instrument that addresses attitudes in seven domains; social implications of science, normality of scientists, attitude toward inquiry, adoption of scientific attitudes, enjoyment of science lessons, leisure interest in science, and career interest in science. Values from 1-50 are obtained for each domain with no overall attitude value assigned. The research found that girls in general had significantly more positive attitudes toward science in all seven of the measured domains and the females from the traditional approach were more positive than the females from the Physics First approach. Girls from the traditional approach also reported intent to take high-level (AP) science courses in their senior year at a significantly higher rate than did the girls in Physics First. Neither science approach showed any significance in the reported intention to pursue a science-related career.

The Integration of Nutrition Education in the Basic Biomedical Sciences

ERIC Educational Resources Information Center

Raw, Isaias

1977-01-01

At the Center for Biomedical Education at the City University of New York, nutrition is integrated into the chemistry-biochemistry sequence of a six-year B.S.-M.D. program. Students perform an actual analysis of a sample of their own food, learning basic techniques and concepts, and also carry on experiments with rats on other diets. (Editor/LBH)

The BIG Data Center: from deposition to integration to translation

PubMed Central

2017-01-01

Biological data are generated at unprecedentedly exponential rates, posing considerable challenges in big data deposition, integration and translation. The BIG Data Center, established at Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, provides a suite of database resources, including (i) Genome Sequence Archive, a data repository specialized for archiving raw sequence reads, (ii) Gene Expression Nebulas, a data portal of gene expression profiles based entirely on RNA-Seq data, (iii) Genome Variation Map, a comprehensive collection of genome variations for featured species, (iv) Genome Warehouse, a centralized resource housing genome-scale data with particular focus on economically important animals and plants, (v) Methylation Bank, an integrated database of whole-genome single-base resolution methylomes and (vi) Science Wikis, a central access point for biological wikis developed for community annotations. The BIG Data Center is dedicated to constructing and maintaining biological databases through big data integration and value-added curation, conducting basic research to translate big data into big knowledge and providing freely open access to a variety of data resources in support of worldwide research activities in both academia and industry. All of these resources are publicly available and can be found at http://bigd.big.ac.cn. PMID:27899658

Intentional research design in implementation science: implications for the use of nomothetic and idiographic assessment.

PubMed

Lyon, Aaron R; Connors, Elizabeth; Jensen-Doss, Amanda; Landes, Sara J; Lewis, Cara C; McLeod, Bryce D; Rutt, Christopher; Stanick, Cameo; Weiner, Bryan J

2017-09-01

The advancement of implementation science is dependent on identifying assessment strategies that can address implementation and clinical outcome variables in ways that are valid, relevant to stakeholders, and scalable. This paper presents a measurement agenda for implementation science that integrates the previously disparate assessment traditions of idiographic and nomothetic approaches. Although idiographic and nomothetic approaches are both used in implementation science, a review of the literature on this topic suggests that their selection can be indiscriminate, driven by convenience, and not explicitly tied to research study design. As a result, they are not typically combined deliberately or effectively. Thoughtful integration may simultaneously enhance both the rigor and relevance of assessments across multiple levels within health service systems. Background on nomothetic and idiographic assessment is provided as well as their potential to support research in implementation science. Drawing from an existing framework, seven structures (of various sequencing and weighting options) and five functions (Convergence, Complementarity, Expansion, Development, Sampling) for integrating conceptually distinct research methods are articulated as they apply to the deliberate, design-driven integration of nomothetic and idiographic assessment approaches. Specific examples and practical guidance are provided to inform research consistent with this framework. Selection and integration of idiographic and nomothetic assessments for implementation science research designs can be improved. The current paper argues for the deliberate application of a clear framework to improve the rigor and relevance of contemporary assessment strategies.

Unraveling the Complexities of Life Sciences Data.

PubMed

Higdon, Roger; Haynes, Winston; Stanberry, Larissa; Stewart, Elizabeth; Yandl, Gregory; Howard, Chris; Broomall, William; Kolker, Natali; Kolker, Eugene

2013-03-01

The life sciences have entered into the realm of big data and data-enabled science, where data can either empower or overwhelm. These data bring the challenges of the 5 Vs of big data: volume, veracity, velocity, variety, and value. Both independently and through our involvement with DELSA Global (Data-Enabled Life Sciences Alliance, DELSAglobal.org), the Kolker Lab ( kolkerlab.org ) is creating partnerships that identify data challenges and solve community needs. We specialize in solutions to complex biological data challenges, as exemplified by the community resource of MOPED (Model Organism Protein Expression Database, MOPED.proteinspire.org ) and the analysis pipeline of SPIRE (Systematic Protein Investigative Research Environment, PROTEINSPIRE.org ). Our collaborative work extends into the computationally intensive tasks of analysis and visualization of millions of protein sequences through innovative implementations of sequence alignment algorithms and creation of the Protein Sequence Universe tool (PSU). Pushing into the future together with our collaborators, our lab is pursuing integration of multi-omics data and exploration of biological pathways, as well as assigning function to proteins and porting solutions to the cloud. Big data have come to the life sciences; discovering the knowledge in the data will bring breakthroughs and benefits.

Implementing Distributed Operations: A Comparison of Two Deep Space Missions

NASA Technical Reports Server (NTRS)

Mishkin, Andrew; Larsen, Barbara

2006-01-01

Two very different deep space exploration missions--Mars Exploration Rover and Cassini--have made use of distributed operations for their science teams. In the case of MER, the distributed operations capability was implemented only after the prime mission was completed, as the rovers continued to operate well in excess of their expected mission lifetimes; Cassini, designed for a mission of more than ten years, had planned for distributed operations from its inception. The rapid command turnaround timeline of MER, as well as many of the operations features implemented to support it, have proven to be conducive to distributed operations. These features include: a single science team leader during the tactical operations timeline, highly integrated science and engineering teams, processes and file structures designed to permit multiple team members to work in parallel to deliver sequencing products, web-based spacecraft status and planning reports for team-wide access, and near-elimination of paper products from the operations process. Additionally, MER has benefited from the initial co-location of its entire operations team, and from having a single Principal Investigator, while Cassini operations have had to reconcile multiple science teams distributed from before launch. Cassini has faced greater challenges in implementing effective distributed operations. Because extensive early planning is required to capture science opportunities on its tour and because sequence development takes significantly longer than sequence execution, multiple teams are contributing to multiple sequences concurrently. The complexity of integrating inputs from multiple teams is exacerbated by spacecraft operability issues and resource contention among the teams, each of which has their own Principal Investigator. Finally, much of the technology that MER has exploited to facilitate distributed operations was not available when the Cassini ground system was designed, although later adoption of web-based and telecommunication tools has been critical to the success of Cassini operations.

Music and language perception: expectations, structural integration, and cognitive sequencing.

PubMed

Tillmann, Barbara

2012-10-01

Music can be described as sequences of events that are structured in pitch and time. Studying music processing provides insight into how complex event sequences are learned, perceived, and represented by the brain. Given the temporal nature of sound, expectations, structural integration, and cognitive sequencing are central in music perception (i.e., which sounds are most likely to come next and at what moment should they occur?). This paper focuses on similarities in music and language cognition research, showing that music cognition research provides insight into the understanding of not only music processing but also language processing and the processing of other structured stimuli. The hypothesis of shared resources between music and language processing and of domain-general dynamic attention has motivated the development of research to test music as a means to stimulate sensory, cognitive, and motor processes. Copyright © 2012 Cognitive Science Society, Inc.

Understanding the Language Demands on Science Students from an Integrated Science and Language Perspective

NASA Astrophysics Data System (ADS)

Seah, Lay Hoon; Clarke, David John; Hart, Christina Eugene

2014-04-01

This case study of a science lesson, on the topic thermal expansion, examines the language demands on students from an integrated science and language perspective. The data were generated during a sequence of 9 lessons on the topic of 'States of Matter' in a Grade 7 classroom (12-13 years old students). We identify the language demands by comparing students' writings with the scientific account of expansion that the teacher intended the students to learn. The comparison involved both content analysis and lexicogrammatical (LG) analysis. The framework of Systemic Functional Linguistics was adopted for the LG analysis. Our analysis reveals differences in the meaning and the way LG resources were employed between the students' writings and the scientific account. From these differences, we found the notion of condition-of-use for LG resources to be a significant aspect of the language that students need to appropriate in order to employ the language of school science appropriately. This notion potentially provides a means by which teachers could concurrently address the conceptual and representational demands of science learning. Finally, we reflect on how the complementary use of content analysis and LG analysis provides a way for integrating the science and language perspectives in order to understand the demands of learning science through language.

High-throughput automated microfluidic sample preparation for accurate microbial genomics

PubMed Central

Kim, Soohong; De Jonghe, Joachim; Kulesa, Anthony B.; Feldman, David; Vatanen, Tommi; Bhattacharyya, Roby P.; Berdy, Brittany; Gomez, James; Nolan, Jill; Epstein, Slava; Blainey, Paul C.

2017-01-01

Low-cost shotgun DNA sequencing is transforming the microbial sciences. Sequencing instruments are so effective that sample preparation is now the key limiting factor. Here, we introduce a microfluidic sample preparation platform that integrates the key steps in cells to sequence library sample preparation for up to 96 samples and reduces DNA input requirements 100-fold while maintaining or improving data quality. The general-purpose microarchitecture we demonstrate supports workflows with arbitrary numbers of reaction and clean-up or capture steps. By reducing the sample quantity requirements, we enabled low-input (∼10,000 cells) whole-genome shotgun (WGS) sequencing of Mycobacterium tuberculosis and soil micro-colonies with superior results. We also leveraged the enhanced throughput to sequence ∼400 clinical Pseudomonas aeruginosa libraries and demonstrate excellent single-nucleotide polymorphism detection performance that explained phenotypically observed antibiotic resistance. Fully-integrated lab-on-chip sample preparation overcomes technical barriers to enable broader deployment of genomics across many basic research and translational applications. PMID:28128213

Earth Systems Science in an Integrated Science Content and Methods Course for Elementary Education Majors

NASA Astrophysics Data System (ADS)

Madsen, J. A.; Allen, D. E.; Donham, R. S.; Fifield, S. J.; Shipman, H. L.; Ford, D. J.; Dagher, Z. R.

2004-12-01

With funding from the National Science Foundation, we have designed an integrated science content and methods course for sophomore-level elementary teacher education (ETE) majors. This course, the Science Semester, is a 15-credit sequence that consists of three science content courses (Earth, Life, and Physical Science) and a science teaching methods course. The goal of this integrated science and education methods curriculum is to foster holistic understandings of science and pedagogy that future elementary teachers need to effectively use inquiry-based approaches in teaching science in their classrooms. During the Science Semester, traditional subject matter boundaries are crossed to stress shared themes that teachers must understand to teach standards-based elementary science. Exemplary approaches that support both learning science and learning how to teach science are used. In the science courses, students work collaboratively on multidisciplinary problem-based learning (PBL) activities that place science concepts in authentic contexts and build learning skills. In the methods course, students critically explore the theory and practice of elementary science teaching, drawing on their shared experiences of inquiry learning in the science courses. An earth system science approach is ideally adapted for the integrated, inquiry-based learning that takes place during the Science Semester. The PBL investigations that are the hallmark of the Science Semester provide the backdrop through which fundamental earth system interactions can be studied. For example in the PBL investigation that focuses on energy, the carbon cycle is examined as it relates to fossil fuels. In another PBL investigation centered on kids, cancer, and the environment, the hydrologic cycle with emphasis on surface runoff and ground water contamination is studied. In a PBL investigation that has students learning about the Delaware Bay ecosystem through the story of the horseshoe crab and the biome that swirls around this remarkable arthropod, students are exposed to interactions between the hydrosphere, atmosphere, and geosphere and they examine ways in which climate change can affect this ecosystem.

The BIG Data Center: from deposition to integration to translation.

PubMed

2017-01-04

Biological data are generated at unprecedentedly exponential rates, posing considerable challenges in big data deposition, integration and translation. The BIG Data Center, established at Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, provides a suite of database resources, including (i) Genome Sequence Archive, a data repository specialized for archiving raw sequence reads, (ii) Gene Expression Nebulas, a data portal of gene expression profiles based entirely on RNA-Seq data, (iii) Genome Variation Map, a comprehensive collection of genome variations for featured species, (iv) Genome Warehouse, a centralized resource housing genome-scale data with particular focus on economically important animals and plants, (v) Methylation Bank, an integrated database of whole-genome single-base resolution methylomes and (vi) Science Wikis, a central access point for biological wikis developed for community annotations. The BIG Data Center is dedicated to constructing and maintaining biological databases through big data integration and value-added curation, conducting basic research to translate big data into big knowledge and providing freely open access to a variety of data resources in support of worldwide research activities in both academia and industry. All of these resources are publicly available and can be found at http://bigd.big.ac.cn. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

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.

[Disciplinar thematic integration in medicine: a proposal from histology and embryology].

PubMed

Bassan, N D; D'Ottavio, A E

2013-01-01

This paper intends to clarify a concept with multiple meanings and a complex reality. It starts providing varied histological and embryological examples apt to contribute the stimulation of teacher and student imaginations in favor of a crucial skill, as thematic integration is, into the present and changing curricula in Medicine in particular and Health Sciences in general. In this sense, it offers linear and branched sequences as well as consolidation graphics which focusing in both disciplines may also include other basic ones, key for clinic diagnosis, among the competences to be developed. After registering some preliminary results revealing the need of its continuous and progressive training along the complete medical career, its own integrative value and the integrative one for their teachers due to its natural link with other basic ones is outlined, its relevance for undergraduate is reaffirmed and possible future variations for them are previewed, considering the present exponential growth of science and technology.

Beyond DNA Sequencing in Space: Current and Future Omics Capabilities of the Biomolecule Sequencer Payload

NASA Technical Reports Server (NTRS)

Wallace, Sarah

2017-01-01

Why do we need a DNA sequencer to support the human exploration of space? (A) Operational environmental monitoring; (1) Identification of contaminating microbes, (2) Infectious disease diagnosis, (3) Reduce down mass (sample return for environmental monitoring, crew health, etc.). (B) Research; (1) Human, (2) Animal, (3) Microbes/Cell lines, (4) Plant. (C) Med Ops; (1) Response to countermeasures, (2) Radiation, (3) Real-time analysis can influence medical intervention. (C) Support astrobiology science investigations; (1) Technology superiorly suited to in situ nucleic acid-based life detection, (2) Functional testing for integration into robotics for extraplanetary exploration mission.

Introductory life science mathematics and quantitative neuroscience courses.

PubMed

Duffus, Dwight; Olifer, Andrei

2010-01-01

We describe two sets of courses designed to enhance the mathematical, statistical, and computational training of life science undergraduates at Emory College. The first course is an introductory sequence in differential and integral calculus, modeling with differential equations, probability, and inferential statistics. The second is an upper-division course in computational neuroscience. We provide a description of each course, detailed syllabi, examples of content, and a brief discussion of the main issues encountered in developing and offering the courses.

Integrating Science, Mathematics, and Sociology in an Inquiry-Based Study of Changing Population Density.

ERIC Educational Resources Information Center

Schlenker, Richard M.; Schlenker, Karl R.

2000-01-01

Presents a five-activity sequence designed to help students understand the effects of population doubling. Activities consider the effects of population doubling on human interactions, drinking water supplies, and food supply. Students also develop graphs of data and write research papers. (WRM)

Integrating Science and Practice in Pharmacy Curricula

PubMed Central

Todd, Adam; Fulton, John

2014-01-01

An integrated curriculum is one where the summation of different academic disciplines forms a coherent whole and, importantly, where the relationships between the different disciplines have been carefully and strategically considered when forming the composite. Within pharmacy curriculum integration is important in order to produce graduates who have the capacity to apply their knowledge to a range of complex problems where available information is often incomplete. This paper discusses the development of an integrated curriculum in which students are presented with an organized, logical sequence of material, but still challenged to make their own integrations and develop as integrative thinkers. An evidence-based model upon which an interdisciplinary undergraduate pharmacy curriculum can be built is presented. PMID:24761024

From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity.

PubMed

Cristescu, Melania E

2014-10-01

DNA-based species identification, known as barcoding, transformed the traditional approach to the study of biodiversity science. The field is transitioning from barcoding individuals to metabarcoding communities. This revolution involves new sequencing technologies, bioinformatics pipelines, computational infrastructure, and experimental designs. In this dynamic genomics landscape, metabarcoding studies remain insular and biodiversity estimates depend on the particular methods used. In this opinion article, I discuss the need for a coordinated advancement of DNA-based species identification that integrates taxonomic and barcoding information. Such an approach would facilitate access to almost 3 centuries of taxonomic knowledge and 1 decade of building repository barcodes. Conservation projects are time sensitive, research funding is becoming restricted, and informed decisions depend on our ability to embrace integrative approaches to biodiversity science. Copyright © 2014 Elsevier Ltd. All rights reserved.

Strategies for automatic planning: A collection of ideas

NASA Technical Reports Server (NTRS)

Collins, Carol; George, Julia; Zamani, Elaine

1989-01-01

The main goal of the Jet Propulsion Laboratory (JPL) is to obtain science return from interplanetary probes. The uplink process is concerned with communicating commands to a spacecraft in order to achieve science objectives. There are two main parts to the development of the command file which is sent to a spacecraft. First, the activity planning process integrates the science requests for utilization of spacecraft time into a feasible sequence. Then the command generation process converts the sequence into a set of commands. The development of a feasible sequence plan is an expensive and labor intensive process requiring many months of effort. In order to save time and manpower in the uplink process, automation of parts of this process is desired. There is an ongoing effort to develop automatic planning systems. This has met with some success, but has also been informative about the nature of this effort. It is now clear that innovative techniques and state-of-the-art technology will be required in order to produce a system which can provide automatic sequence planning. As part of this effort to develop automatic planning systems, a survey of the literature, looking for known techniques which may be applicable to our work was conducted. Descriptions of and references for these methods are given, together with ideas for applying the techniques to automatic planning.

Anatomy integration blueprint: A fourth-year musculoskeletal anatomy elective model.

PubMed

Lazarus, Michelle D; Kauffman, Gordon L; Kothari, Milind J; Mosher, Timothy J; Silvis, Matthew L; Wawrzyniak, John R; Anderson, Daniel T; Black, Kevin P

2014-01-01

Current undergraduate medical school curricular trends focus on both vertical integration of clinical knowledge into the traditionally basic science-dedicated curricula and increasing basic science education in the clinical years. This latter type of integration is more difficult and less reported on than the former. Here, we present an outline of a course wherein the primary learning and teaching objective is to integrate basic science anatomy knowledge with clinical education. The course was developed through collaboration by a multi-specialist course development team (composed of both basic scientists and physicians) and was founded in current adult learning theories. The course was designed to be widely applicable to multiple future specialties, using current published reports regarding the topics and clinical care areas relying heavily on anatomical knowledge regardless of specialist focus. To this end, the course focuses on the role of anatomy in the diagnosis and treatment of frequently encountered musculoskeletal conditions. Our iterative implementation and action research approach to this course development has yielded a curricular template for anatomy integration into clinical years. Key components for successful implementation of these types of courses, including content topic sequence, the faculty development team, learning approaches, and hidden curricula, were developed. We also report preliminary feedback from course stakeholders and lessons learned through the process. The purpose of this report is to enhance the current literature regarding basic science integration in the clinical years of medical school. © 2014 American Association of Anatomists.

Introductory Life Science Mathematics and Quantitative Neuroscience Courses

PubMed Central

Olifer, Andrei

2010-01-01

We describe two sets of courses designed to enhance the mathematical, statistical, and computational training of life science undergraduates at Emory College. The first course is an introductory sequence in differential and integral calculus, modeling with differential equations, probability, and inferential statistics. The second is an upper-division course in computational neuroscience. We provide a description of each course, detailed syllabi, examples of content, and a brief discussion of the main issues encountered in developing and offering the courses. PMID:20810971

Seeking Synthesis: The Integrative Problem in Understanding Language and Its Evolution.

PubMed

Dale, Rick; Kello, Christopher T; Schoenemann, P Thomas

2016-04-01

We discuss two problems for a general scientific understanding of language, sequences and synergies: how language is an intricately sequenced behavior and how language is manifested as a multidimensionally structured behavior. Though both are central in our understanding, we observe that the former tends to be studied more than the latter. We consider very general conditions that hold in human brain evolution and its computational implications, and identify multimodal and multiscale organization as two key characteristics of emerging cognitive function in our species. This suggests that human brains, and cognitive function specifically, became more adept at integrating diverse information sources and operating at multiple levels for linguistic performance. We argue that framing language evolution, learning, and use in terms of synergies suggests new research questions, and it may be a fruitful direction for new developments in theory and modeling of language as an integrated system. Copyright © 2016 Cognitive Science Society, Inc.

Investigating the Effectiveness of Computer Simulations for Chemistry Learning

ERIC Educational Resources Information Center

Plass, Jan L.; Milne, Catherine; Homer, Bruce D.; Schwartz, Ruth N.; Hayward, Elizabeth O.; Jordan, Trace; Verkuilen, Jay; Ng, Florrie; Wang, Yan; Barrientos, Juan

2012-01-01

Are well-designed computer simulations an effective tool to support student understanding of complex concepts in chemistry when integrated into high school science classrooms? We investigated scaling up the use of a sequence of simulations of kinetic molecular theory and associated topics of diffusion, gas laws, and phase change, which we designed…

Neo-Darwinism, the Modern Synthesis and selfish genes: are they of use in physiology?

PubMed Central

Noble, Denis

2011-01-01

This article argues that the gene-centric interpretations of evolution, and more particularly the selfish gene expression of those interpretations, form barriers to the integration of physiological science with evolutionary theory. A gene-centred approach analyses the relationships between genotypes and phenotypes in terms of differences (change the genotype and observe changes in phenotype). We now know that, most frequently, this does not correctly reveal the relationships because of extensive buffering by robust networks of interactions. By contrast, understanding biological function through physiological analysis requires an integrative approach in which the activity of the proteins and RNAs formed from each DNA template is analysed in networks of interactions. These networks also include components that are not specified by nuclear DNA. Inheritance is not through DNA sequences alone. The selfish gene idea is not useful in the physiological sciences, since selfishness cannot be defined as an intrinsic property of nucleotide sequences independently of gene frequency, i.e. the ‘success’ in the gene pool that is supposed to be attributable to the ‘selfish’ property. It is not a physiologically testable hypothesis. PMID:21135048

Neo-Darwinism, the modern synthesis and selfish genes: are they of use in physiology?

PubMed

Noble, Denis

2011-03-01

This article argues that the gene-centric interpretations of evolution, and more particularly the selfish gene expression of those interpretations, form barriers to the integration of physiological science with evolutionary theory. A gene-centred approach analyses the relationships between genotypes and phenotypes in terms of differences (change the genotype and observe changes in phenotype). We now know that, most frequently, this does not correctly reveal the relationships because of extensive buffering by robust networks of interactions. By contrast, understanding biological function through physiological analysis requires an integrative approach in which the activity of the proteins and RNAs formed from each DNA template is analysed in networks of interactions. These networks also include components that are not specified by nuclear DNA. Inheritance is not through DNA sequences alone. The selfish gene idea is not useful in the physiological sciences, since selfishness cannot be defined as an intrinsic property of nucleotide sequences independently of gene frequency, i.e. the 'success' in the gene pool that is supposed to be attributable to the 'selfish' property. It is not a physiologically testable hypothesis.

Science sequence design

NASA Technical Reports Server (NTRS)

Koskela, P. E.; Bollman, W. E.; Freeman, J. E.; Helton, M. R.; Reichert, R. J.; Travers, E. S.; Zawacki, S. J.

1973-01-01

The activities of the following members of the Navigation Team are recorded: the Science Sequence Design Group, responsible for preparing the final science sequence designs; the Advanced Sequence Planning Group, responsible for sequence planning; and the Science Recommendation Team (SRT) representatives, responsible for conducting the necessary sequence design interfaces with the teams during the mission. The interface task included science support in both advance planning and daily operations. Science sequences designed during the mission are also discussed.

Integrating Genetics and Social Science: Genetic Risk Scores

PubMed Central

Belsky, Daniel W.; Israel, Salomon

2014-01-01

The sequencing of the human genome and the advent of low-cost genome-wide assays that generate millions of observations of individual genomes in a matter of hours constitute a disruptive innovation for social science. Many public-use social science datasets have or will soon add genome-wide genetic data. With these new data come technical challenges, but also new possibilities. Among these, the lowest hanging fruit and the most potentially disruptive to existing research programs is the ability to measure previously invisible contours of health and disease risk within populations. In this article, we outline why now is the time for social scientists to bring genetics into their research programs. We discuss how to select genetic variants to study. We explain how the polygenic architecture of complex traits and the low penetrance of individual genetic loci pose challenges to research integrating genetics and social science. We introduce genetic risk scores as a method of addressing these challenges and provide guidance on how genetic risk scores can be constructed. We conclude by outlining research questions that are ripe for social science inquiry. PMID:25343363

Semantic integration of information about orthologs and diseases: the OGO system.

PubMed

Miñarro-Gimenez, Jose Antonio; Egaña Aranguren, Mikel; Martínez Béjar, Rodrigo; Fernández-Breis, Jesualdo Tomás; Madrid, Marisa

2011-12-01

Semantic Web technologies like RDF and OWL are currently applied in life sciences to improve knowledge management by integrating disparate information. Many of the systems that perform such task, however, only offer a SPARQL query interface, which is difficult to use for life scientists. We present the OGO system, which consists of a knowledge base that integrates information of orthologous sequences and genetic diseases, providing an easy to use ontology-constrain driven query interface. Such interface allows the users to define SPARQL queries through a graphical process, therefore not requiring SPARQL expertise. Copyright © 2011 Elsevier Inc. All rights reserved.

Integrating Inquiry-Based Science and Education Methods Courses in a "Science Semester" for Future Elementary Teachers

NASA Astrophysics Data System (ADS)

Madsen, J.; Fifield, S.; Allen, D.; Brickhouse, N.; Dagher, Z.; Ford, D.; Shipman, H.

2001-05-01

In this NSF-funded project we will adapt problem-based learning (PBL) and other inquiry-based approaches to create an integrated science and education methods curriculum ("science semester") for elementary teacher education majors. Our goal is to foster integrated understandings of science and pedagogy that future elementary teachers need to effectively use inquiry-based approaches in their classrooms. This project responds to calls to improve science education for all students by making preservice teachers' experiences in undergraduate science courses more consistent with reforms at the K-12 level. The involved faculty teach three science courses (biology, earth science, physical science) and an elementary science education methods course that are degree requirements for elementary teacher education majors. Presently, students take the courses in variable sequences and at widely scattered times. Too many students fail to appreciate the value of science courses to their future careers as teachers, and when they reach the methods course in the junior year they often retain little of the science content studied earlier. These episodic encounters with science make it difficult for students to learn the content, and to translate their understandings of science into effective, inquiry-based teaching strategies. To encourage integrated understandings of science concepts and pedagogy we will coordinate the science and methods courses in a junior-year science semester. Traditional subject matter boundaries will be crossed to stress shared themes that teachers must understand to teach standards-based elementary science. We will adapt exemplary approaches that support both learning science and learning how to teach science. Students will work collaboratively on multidisciplinary PBL activities that place science concepts in authentic contexts and build learning skills. "Lecture" meetings will be large group active learning sessions that help students understand difficult concepts, make connections between class activities, and launch and wrap-up PBL problems. Labs will include activities from elementary science kits as launching points for in-depth investigations that demonstrate the continuity of science concepts and pedagogies across age levels. In the methods course, students will critically explore the theory and practice of elementary science teaching, drawing on their shared experiences of inquiry learning in the science courses. Field placements in elementary classrooms will allow students to ground their studies of science and pedagogy in actual practice.

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

ERIC Educational Resources Information Center

Scott, Arthur; And Others

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

Standards for Technological Literacy and STEM Education Delivery through Career and Technical Education Programs

ERIC Educational Resources Information Center

Asunda, Paul A.

2012-01-01

At a minimum, employers rely on career and technical education (CTE) and workforce training systems to supply workers able to perform in their jobs. In CTE classes that seek to integrate science, technology, engineering, and mathematics (STEM) concepts, it falls to the instructors to design and sequence the learning experiences that will promote…

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

ERIC Educational Resources Information Center

Jarvis, Bruce; Mazzocchi, Paul; Hearle, Robert

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

Brain Region-Specific Expression of Genes Mapped within Quantitative Trait Loci for Behavioral Responsiveness to Acute Stress in Fisher 344 and Wistar Kyoto Male Rats (Open Access Postprint)

DTIC Science & Technology

2018-03-12

RGSC_3.4. Using the Integrative Genomics Viewer (Broad Institute, Cambridge, Massachusetts), we iden- tified the coding sequence variations between the...adrenal axis abnormalities and disturbances in brain metabolism resem- bling those in depressive states [74]. Ifna2 is also known to induce memory... psychological science a journal of the Association for Psychological Science. 2016; 4(1):17–27. https://doi.org/10.1177/2167702615577470 PMID: 26958455

Unlimited Thirst for Genome Sequencing, Data Interpretation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant Improvement

PubMed Central

Govindaraj, Mahalingam

2015-01-01

The number of sequenced crop genomes and associated genomic resources is growing rapidly with the advent of inexpensive next generation sequencing methods. Databases have become an integral part of all aspects of science research, including basic and applied plant and animal sciences. The importance of databases keeps increasing as the volume of datasets from direct and indirect genomics, as well as other omics approaches, keeps expanding in recent years. The databases and associated web portals provide at a minimum a uniform set of tools and automated analysis across a wide range of crop plant genomes. This paper reviews some basic terms and considerations in dealing with crop plant databases utilization in advancing genomic era. The utilization of databases for variation analysis with other comparative genomics tools, and data interpretation platforms are well described. The major focus of this review is to provide knowledge on platforms and databases for genome-based investigations of agriculturally important crop plants. The utilization of these databases in applied crop improvement program is still being achieved widely; otherwise, the end for sequencing is not far away. PMID:25874133

Modeling of the Orbital Evolution of 2060 Chiron

NASA Astrophysics Data System (ADS)

Kovalenko, Nataliya S.; Babenko, Yury G.; Churyumov, Klim I.

2002-03-01

The origin of Centaurs is one of the most interesting problems of Solar system science, and it has not yet been solved. To shed light on this problem one can investigate Centaurs' past and future orbital evolution. In this paper we discuss the results of Chiron's orbital evolution modeling. It was the first discovered Centaur and is the brightest one. Numerical integration was produced for 1 Myr forward and backward from the present time. A program based on the Everhart single sequence method for integrating orbits was used.

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

PubMed Central

Kearse, Matthew; Moir, Richard; Wilson, Amy; Stones-Havas, Steven; Cheung, Matthew; Sturrock, Shane; Buxton, Simon; Cooper, Alex; Markowitz, Sidney; Duran, Chris; Thierer, Tobias; Ashton, Bruce; Meintjes, Peter; Drummond, Alexei

2012-01-01

Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com PMID:22543367

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.

PubMed

Kearse, Matthew; Moir, Richard; Wilson, Amy; Stones-Havas, Steven; Cheung, Matthew; Sturrock, Shane; Buxton, Simon; Cooper, Alex; Markowitz, Sidney; Duran, Chris; Thierer, Tobias; Ashton, Bruce; Meintjes, Peter; Drummond, Alexei

2012-06-15

The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.

Integrative taxonomy helps to reveal the mask of the genus Gynandropaa (Amphibia: Anura: Dicroglossidae).

PubMed

Huang, Yan; Hu, Junhua; Wang, Bin; Song, Zhaobin; Zhou, Caiquan; Jiang, Jianping

2016-03-01

Species of the genus Gynandropaa within the family Dicroglossidae are typical spiny frogs whose taxonomic status has long been in doubt. We used integrative methods, involving morphological and molecular analyses, to elucidate the phylogenetic relationships, and to determine identities and the geographic distribution of each valid species. We obtained DNA sequence data of 5 species of Gynandropaa (complete sequences of the mitochondrial NADH dehydrogenase subunit 2 [ND2] gene, and 890 bp of 12S rRNA and 16S rRNA partial sequences) from 37 localities (including the topotypes of 5 described species) and constructed Bayesian and maximum-likelihood trees to examine the patterns of phylogeography. A total of 28 morphological variables were taken on 624 specimens. Three clades with clear geographic patterns were recognized: clade C (from south-western Sichuan Province and central Yunnan Province), clade E (western Guizhou Province and eastern to central Yunnan Province) and clade W (western to southern Yunnan Province). Integrating morphological characteristics and distribution information, the clades W, E and C represent Gynandropaa yunnanensis, G. phrynoides and G. sichuanensis, respectively. We draw the following conclusions: (i) the taxon G. phrynoides, formerly evaluated as a junior synonym of G. yunnanensis, is revalidated herein at the rank of species; (ii) G. liui is a junior synonym of G. sichuanensis; and (iii) G. yunnanensis is a valid species while G. bourreti is probably a subspecies of G. yunnanensis, with the distribution range from Vietnam to southern Yunnan Province. This study clears up the taxonomic status of Gynandropaa and provides important information for understanding the evolution and conservation of these spiny frogs. © 2015 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.

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

ERIC Educational Resources Information Center

Ohio State Univ., Columbus. Cooperative Extension Service.

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

Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases.

PubMed

Kobayashi, Norio; Ishii, Manabu; Takahashi, Satoshi; Mochizuki, Yoshiki; Matsushima, Akihiro; Toyoda, Tetsuro

2011-07-01

Global cloud frameworks for bioinformatics research databases become huge and heterogeneous; solutions face various diametric challenges comprising cross-integration, retrieval, security and openness. To address this, as of March 2011 organizations including RIKEN published 192 mammalian, plant and protein life sciences databases having 8.2 million data records, integrated as Linked Open or Private Data (LOD/LPD) using SciNetS.org, the Scientists' Networking System. The huge quantity of linked data this database integration framework covers is based on the Semantic Web, where researchers collaborate by managing metadata across public and private databases in a secured data space. This outstripped the data query capacity of existing interface tools like SPARQL. Actual research also requires specialized tools for data analysis using raw original data. To solve these challenges, in December 2009 we developed the lightweight Semantic-JSON interface to access each fragment of linked and raw life sciences data securely under the control of programming languages popularly used by bioinformaticians such as Perl and Ruby. Researchers successfully used the interface across 28 million semantic relationships for biological applications including genome design, sequence processing, inference over phenotype databases, full-text search indexing and human-readable contents like ontology and LOD tree viewers. Semantic-JSON services of SciNetS.org are provided at http://semanticjson.org.

Forecasting Ecological Genomics: High-Tech Animal Instrumentation Meets High-Throughput Sequencing

PubMed Central

Shafer, Aaron B. A.; Northrup, Joseph M.; Wikelski, Martin; Wittemyer, George; Wolf, Jochen B. W.

2016-01-01

Recent advancements in animal tracking technology and high-throughput sequencing are rapidly changing the questions and scope of research in the biological sciences. The integration of genomic data with high-tech animal instrumentation comes as a natural progression of traditional work in ecological genetics, and we provide a framework for linking the separate data streams from these technologies. Such a merger will elucidate the genetic basis of adaptive behaviors like migration and hibernation and advance our understanding of fundamental ecological and evolutionary processes such as pathogen transmission, population responses to environmental change, and communication in natural populations. PMID:26745372

A Roadmap for using Agile Development in a Traditional System

NASA Technical Reports Server (NTRS)

Streiffert, Barbara; Starbird, Thomas

2006-01-01

I. Ensemble Development Group: a) Produces activity planning software for in spacecraft; b) Built on Eclipse Rich Client Platform (open source development and runtime software); c) Funded by multiple sources including the Mars Technology Program; d) Incorporated the use of Agile Development. II. Next Generation Uplink Planning System: a) Researches the Activity Planning and Sequencing Subsystem for Mars Science Laboratory (APSS); b) APSS includes Ensemble, Activity Modeling, Constraint Checking, Command Editing and Sequencing tools plus other uplink generation utilities; c) Funded by the Mars Technology Program; d) Integrates all of the tools for APSS.

A pedagogical example of second-order arithmetic sequences applied to the construction of computer passwords by upper elementary grade students

NASA Astrophysics Data System (ADS)

Coggins, Porter E.

2015-04-01

The purpose of this paper is (1) to present how general education elementary school age students constructed computer passwords using digital root sums and second-order arithmetic sequences, (2) argue that computer password construction can be used as an engaging introduction to generate interest in elementary school students to study mathematics related to computer science, and (3) share additional mathematical ideas accessible to elementary school students that can be used to create computer passwords. This paper serves to fill a current gap in the literature regarding the integration of mathematical content accessible to upper elementary school students and aspects of computer science in general, and computer password construction in particular. In addition, the protocols presented here can serve as a hook to generate further interest in mathematics and computer science. Students learned to create a random-looking computer password by using biometric measurements of their shoe size, height, and age in months and to create a second-order arithmetic sequence, then converted the resulting numbers into characters that become their computer passwords. This password protocol can be used to introduce students to good computer password habits that can serve a foundation for a life-long awareness of data security. A refinement of the password protocol is also presented.

Developing a yearlong Next Generation Science Standard (NGSS) learning sequence focused on climate solutions: opportunities, challenges and reflections

NASA Astrophysics Data System (ADS)

Cordero, E.; Centeno, D.

2015-12-01

Over the last four years, the Green Ninja Project (GNP) has been developing educational media (e.g., videos, games and online lessons) to help motivate student interest and engagement around climate science and solutions. Inspired by the new emphasis in NGSS on climate change, human impact and engineering design, the GNP is developing a technology focused, integrative, and yearlong science curriculum focused around solutions to climate change. Recognizing the importance of teacher training on the successful implementation of NGSS, we have also integrated teacher professional development into our curriculum. During the presentation, we will describe the design philosophy around our middle school curriculum and share data from a series of classes that are piloting the curriculum during Fall 2015. We will also share our perspectives on how data, media creation and engineering can be used to create educational experiences that model the type of 'three-dimensional learning' encouraged by NGSS.

Application Architecture of Avian Influenza Research Collaboration Network in Korea e-Science

NASA Astrophysics Data System (ADS)

Choi, Hoon; Lee, Junehawk

In the pursuit of globalization of the AI e-Science environment, KISTI is fostering to extend the AI research community to the AI research institutes of neighboring countries and to share the AI e-Science environment with them in the near future. In this paper we introduce the application architecture of AI research collaboration network (AIRCoN). AIRCoN is a global e-Science environment for AI research conducted by KISTI. It consists of AI virus sequence information sharing system for sufficing data requirement of research community, integrated analysis environment for analyzing the mutation pattern of AI viruses and their risks, epidemic modeling and simulation environment for establishing national effective readiness strategy against AI pandemics, and knowledge portal for sharing expertise of epidemic study and unpublished research results with community members.

Robot Sequencing and Visualization Program (RSVP)

NASA Technical Reports Server (NTRS)

Cooper, Brian K.; Maxwell,Scott A.; Hartman, Frank R.; Wright, John R.; Yen, Jeng; Toole, Nicholas T.; Gorjian, Zareh; Morrison, Jack C

2013-01-01

The Robot Sequencing and Visualization Program (RSVP) is being used in the Mars Science Laboratory (MSL) mission for downlink data visualization and command sequence generation. RSVP reads and writes downlink data products from the operations data server (ODS) and writes uplink data products to the ODS. The primary users of RSVP are members of the Rover Planner team (part of the Integrated Planning and Execution Team (IPE)), who use it to perform traversability/articulation analyses, take activity plan input from the Science and Mission Planning teams, and create a set of rover sequences to be sent to the rover every sol. The primary inputs to RSVP are downlink data products and activity plans in the ODS database. The primary outputs are command sequences to be placed in the ODS for further processing prior to uplink to each rover. RSVP is composed of two main subsystems. The first, called the Robot Sequence Editor (RoSE), understands the MSL activity and command dictionaries and takes care of converting incoming activity level inputs into command sequences. The Rover Planners use the RoSE component of RSVP to put together command sequences and to view and manage command level resources like time, power, temperature, etc. (via a transparent realtime connection to SEQGEN). The second component of RSVP is called HyperDrive, a set of high-fidelity computer graphics displays of the Martian surface in 3D and in stereo. The Rover Planners can explore the environment around the rover, create commands related to motion of all kinds, and see the simulated result of those commands via its underlying tight coupling with flight navigation, motor, and arm software. This software is the evolutionary replacement for the Rover Sequencing and Visualization software used to create command sequences (and visualize the Martian surface) for the Mars Exploration Rover mission.

Low-Cost SIRTF Flight Operations

NASA Astrophysics Data System (ADS)

Deutsch, M.-J.; Ebersole, M.; Nichols, J.

1997-12-01

The Space Infrared Telescope Facility (SIRTF) , the fourth of the Great Observatories, will be placed in a unique solar orbit trailing the Earth, in 2001. SIRTF will acquire both imaging and spectral data using large infrared detector arrays from 3.5mm to 160mm. The primary science objectives are (1) search for and study of brown dwarfs and super planets, (2) discovery and study of protoplanetary debris disks, (3) study of ultraluminous galaxies and active galactic nuclei, and (4) study of the early Universe. Driven by the limited cryogenic lifetime of 2.5 years, with a goal of 5 years, and the severely cost-capped development, a Mission Planning and Operations system is being designed that will result in high on-board efficiency (>90%) and low-cost operation, yet will accommodate rapid response science requirements . SIRTF is designing an architecture for an operations system that will be shared between science and flight operations. Crucial to this effort is the philosophy of an integrated science and engineering plan, co-location, cross-training of teams and common planning tools. The common tool set will enable the automatic generation of an integrated and conflict free planned schedule accommodating 20 000 observations and engineering activities a year. The shared tool set will help generate standard observations , (sometimes non-standard) engineering activities and manage the ground and flight resources and constraints appropriately. The ground software will allow the development from the ground of robust event driven sequences. Flexibility will be provided to incorporate newly discovered science opportunities or health issues late in the process and via quick links. This shared science and flight operations process if used from observation selection through sequence and command generation, will provide a low-cost operations system. Though SIRTF is a 'Great Observatory', its annual mission operations costs will more closely resemble those of an Explorer class mission.

A WorkFlow Engine Oriented Modeling System for Hydrologic Sciences

NASA Astrophysics Data System (ADS)

Lu, B.; Piasecki, M.

2009-12-01

In recent years the use of workflow engines for carrying out modeling and data analyses tasks has gained increased attention in the science and engineering communities. Tasks like processing raw data coming from sensors and passing these raw data streams to filters for QA/QC procedures possibly require multiple and complicated steps that need to be repeated over and over again. A workflow sequence that carries out a number of steps of various complexity is an ideal approach to deal with these tasks because the sequence can be stored, called up and repeated over again and again. This has several advantages: for one it ensures repeatability of processing steps and with that provenance, an issue that is increasingly important in the science and engineering communities. It also permits the hand off of lengthy and time consuming tasks that can be error prone to a chain of processing actions that are carried out automatically thus reducing the chance for error on the one side and freeing up time to carry out other tasks on the other hand. This paper aims to present the development of a workflow engine embedded modeling system which allows to build up working sequences for carrying out numerical modeling tasks regarding to hydrologic science. Trident, which facilitates creating, running and sharing scientific data analysis workflows, is taken as the central working engine of the modeling system. Current existing functionalities of the modeling system involve digital watershed processing, online data retrieval, hydrologic simulation and post-event analysis. They are stored as sequences or modules respectively. The sequences can be invoked to implement their preset tasks in orders, for example, triangulating a watershed from raw DEM. Whereas the modules encapsulated certain functions can be selected and connected through a GUI workboard to form sequences. This modeling system is demonstrated by setting up a new sequence for simulating rainfall-runoff processes which involves embedded Penn State Integrated Hydrologic Model(PIHM) module for hydrologic simulation as a kernel, DEM processing sub-sequence which prepares geospatial data for PIHM, data retrieval module which access time series data from online data repository via web services or from local database, post- data management module which stores , visualizes and analyzes model outputs.

Rapid DNA Sequencing by Direct Nanoscale Reading of Nucleotide Bases on Individual DNA Chains

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

Lee, James Weifu; Meller, Amit

2007-01-01

Since the independent invention of DNA sequencing by Sanger and by Gilbert 30 years ago, it has grown from a small scale technique capable of reading several kilobase-pair of sequence per day into today's multibillion dollar industry. This growth has spurred the development of new sequencing technologies that do not involve either electrophoresis or Sanger sequencing chemistries. Sequencing by Synthesis (SBS) involves multiple parallel micro-sequencing addition events occurring on a surface, where data from each round is detected by imaging. New High Throughput Technologies for DNA Sequencing and Genomics is the second volume in the Perspectives in Bioanalysis series, whichmore » looks at the electroanalytical chemistry of nucleic acids and proteins, development of electrochemical sensors and their application in biomedicine and in the new fields of genomics and proteomics. The authors have expertly formatted the information for a wide variety of readers, including new developments that will inspire students and young scientists to create new tools for science and medicine in the 21st century. Reviews of complementary developments in Sanger and SBS sequencing chemistries, capillary electrophoresis and microdevice integration, MS sequencing and applications set the framework for the book.« less

Communicating the Benefits of a Full Sequence of High School Science Courses

ERIC Educational Resources Information Center

Nicholas, Catherine Marie

2014-01-01

High school students are generally uninformed about the benefits of enrolling in a full sequence of science courses, therefore only about a third of our nation's high school graduates have completed the science sequence of Biology, Chemistry and Physics. The lack of students completing a full sequence of science courses contributes to the deficit…

Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases

PubMed Central

Kobayashi, Norio; Ishii, Manabu; Takahashi, Satoshi; Mochizuki, Yoshiki; Matsushima, Akihiro; Toyoda, Tetsuro

2011-01-01

Global cloud frameworks for bioinformatics research databases become huge and heterogeneous; solutions face various diametric challenges comprising cross-integration, retrieval, security and openness. To address this, as of March 2011 organizations including RIKEN published 192 mammalian, plant and protein life sciences databases having 8.2 million data records, integrated as Linked Open or Private Data (LOD/LPD) using SciNetS.org, the Scientists' Networking System. The huge quantity of linked data this database integration framework covers is based on the Semantic Web, where researchers collaborate by managing metadata across public and private databases in a secured data space. This outstripped the data query capacity of existing interface tools like SPARQL. Actual research also requires specialized tools for data analysis using raw original data. To solve these challenges, in December 2009 we developed the lightweight Semantic-JSON interface to access each fragment of linked and raw life sciences data securely under the control of programming languages popularly used by bioinformaticians such as Perl and Ruby. Researchers successfully used the interface across 28 million semantic relationships for biological applications including genome design, sequence processing, inference over phenotype databases, full-text search indexing and human-readable contents like ontology and LOD tree viewers. Semantic-JSON services of SciNetS.org are provided at http://semanticjson.org. PMID:21632604

A readout integrated circuit based on DBI-CTIA and cyclic ADC for MEMS-array-based focal plane

NASA Astrophysics Data System (ADS)

Miao, Liu; Dong, Wu; Zheyao, Wang

2016-11-01

A readout integrated circuit (ROIC) for a MEMS (microelectromechanical system)-array-based focal plane (MAFP) intended for imaging applications is presented. The ROIC incorporates current sources for diode detectors, scanners, timing sequence controllers, differential buffered injection-capacitive trans-impedance amplifier (DBI-CTIA) and 10-bit cyclic ADCs, and is integrated with MAFP using 3-D integration technology. A small-signal equivalent model is built to include thermal detectors into circuit simulations. The biasing current is optimized in terms of signal-to-noise ratio and power consumption. Layout design is tailored to fulfill the requirements of 3-D integration and to adapt to the size of MAFP elements, with not all but only the 2 bottom metal layers to complete nearly all the interconnections in DBI-CTIA and ADC in a 40 μm wide column. Experimental chips are designed and fabricated in a 0.35 μm CMOS mixed signal process, and verified in a code density test of which the results indicate a (0.29/-0.31) LSB differential nonlinearity (DNL) and a (0.61/-0.45) LSB integral nonlinearity (INL). Spectrum analysis shows that the effective number of bits (ENOB) is 9.09. The ROIC consumes 248 mW of power at most if not to cut off quiescent current paths when not needed. Project supported by by National Natural Science Foundation of China (No. 61271130), the Beijing Municipal Science and Tech Project (No. D13110100290000), the Tsinghua University Initiative Scientific Research Program (No. 20131089225), and the Shenzhen Science and Technology Development Fund (No. CXZZ20130322170740736).

VaProS: a database-integration approach for protein/genome information retrieval.

PubMed

Gojobori, Takashi; Ikeo, Kazuho; Katayama, Yukie; Kawabata, Takeshi; Kinjo, Akira R; Kinoshita, Kengo; Kwon, Yeondae; Migita, Ohsuke; Mizutani, Hisashi; Muraoka, Masafumi; Nagata, Koji; Omori, Satoshi; Sugawara, Hideaki; Yamada, Daichi; Yura, Kei

2016-12-01

Life science research now heavily relies on all sorts of databases for genome sequences, transcription, protein three-dimensional (3D) structures, protein-protein interactions, phenotypes and so forth. The knowledge accumulated by all the omics research is so vast that a computer-aided search of data is now a prerequisite for starting a new study. In addition, a combinatory search throughout these databases has a chance to extract new ideas and new hypotheses that can be examined by wet-lab experiments. By virtually integrating the related databases on the Internet, we have built a new web application that facilitates life science researchers for retrieving experts' knowledge stored in the databases and for building a new hypothesis of the research target. This web application, named VaProS, puts stress on the interconnection between the functional information of genome sequences and protein 3D structures, such as structural effect of the gene mutation. In this manuscript, we present the notion of VaProS, the databases and tools that can be accessed without any knowledge of database locations and data formats, and the power of search exemplified in quest of the molecular mechanisms of lysosomal storage disease. VaProS can be freely accessed at http://p4d-info.nig.ac.jp/vapros/ .

Ways of seeing: using the visual arts in nursing education.

PubMed

Frei, Judith; Alvarez, Sarah E; Alexander, Michelle B

2010-12-01

Professional nursing defines its foundation of practice as embedded in the sciences and humanities of a liberal education. This liberal education is commonly alluded to with the phrase "the art and science of nursing." Yet how do we as nursing educators integrate these two concepts? This article describes a method of integrating the humanities as part of an innovative clinical experience. A defined visual art experience was used to improve professional nursing students' observational and communication skills, narrative sequencing abilities, and empathy. The nursing and medical literature describing the use of visual art encounters in health care education is reviewed. The incorporation of an art education program into the curriculum of a cohort of accelerated baccalaureate nursing students is described. Qualitative evaluation measures from the students suggest this was an experience that broadened their understanding of patient encounters. Copyright 2010, SLACK Incorporated.

Integrated optimization of planetary rover layout and exploration routes

NASA Astrophysics Data System (ADS)

Lee, Dongoo; Ahn, Jaemyung

2018-01-01

This article introduces an optimization framework for the integrated design of a planetary surface rover and its exploration route that is applicable to the initial phase of a planetary exploration campaign composed of multiple surface missions. The scientific capability and the mobility of a rover are modelled as functions of the science weight fraction, a key parameter characterizing the rover. The proposed problem is formulated as a mixed-integer nonlinear program that maximizes the sum of profits obtained through a planetary surface exploration mission by simultaneously determining the science weight fraction of the rover, the sites to visit and their visiting sequences under resource consumption constraints imposed on each route and collectively on a mission. A solution procedure for the proposed problem composed of two loops (the outer loop and the inner loop) is developed. The results of test cases demonstrating the effectiveness of the proposed framework are presented.

Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights.

PubMed

Bertelli, Claire; Aeby, Sébastien; Chassot, Bérénice; Clulow, James; Hilfiker, Olivier; Rappo, Samuel; Ritzmann, Sébastien; Schumacher, Paolo; Terrettaz, Céline; Benaglio, Paola; Falquet, Laurent; Farinelli, Laurent; Gharib, Walid H; Goesmann, Alexander; Harshman, Keith; Linke, Burkhard; Miyazaki, Ryo; Rivolta, Carlo; Robinson-Rechavi, Marc; van der Meer, Jan Roelof; Greub, Gilbert

2015-01-01

With the widespread availability of high-throughput sequencing technologies, sequencing projects have become pervasive in the molecular life sciences. The huge bulk of data generated daily must be analyzed further by biologists with skills in bioinformatics and by "embedded bioinformaticians," i.e., bioinformaticians integrated in wet lab research groups. Thus, students interested in molecular life sciences must be trained in the main steps of genomics: sequencing, assembly, annotation and analysis. To reach that goal, a practical course has been set up for master students at the University of Lausanne: the "Sequence a genome" class. At the beginning of the academic year, a few bacterial species whose genome is unknown are provided to the students, who sequence and assemble the genome(s) and perform manual annotation. Here, we report the progress of the first class from September 2010 to June 2011 and the results obtained by seven master students who specifically assembled and annotated the genome of Estrella lausannensis, an obligate intracellular bacterium related to Chlamydia. The draft genome of Estrella is composed of 29 scaffolds encompassing 2,819,825 bp that encode for 2233 putative proteins. Estrella also possesses a 9136 bp plasmid that encodes for 14 genes, among which we found an integrase and a toxin/antitoxin module. Like all other members of the Chlamydiales order, Estrella possesses a highly conserved type III secretion system, considered as a key virulence factor. The annotation of the Estrella genome also allowed the characterization of the metabolic abilities of this strictly intracellular bacterium. Altogether, the students provided the scientific community with the Estrella genome sequence and a preliminary understanding of the biology of this recently-discovered bacterial genus, while learning to use cutting-edge technologies for sequencing and to perform bioinformatics analyses.

What does physics have to do with cancer?

PubMed Central

Michor, Franziska; Liphardt, Jan; Ferrari, Mauro; Widom, Jonathan

2013-01-01

Large-scale cancer genomics, proteomics and RNA-sequencing efforts are currently mapping in fine detail the genetic and biochemical alterations that occur in cancer. However, it is becoming clear that it is difficult to integrate and interpret these data and to translate them into treatments. This difficulty is compounded by the recognition that cancer cells evolve, and that initiation, progression and metastasis are influenced by a wide variety of factors. To help tackle this challenge, the US National Cancer Institute Physical Sciences-Oncology Centers initiative is bringing together physicists, cancer biologists, chemists, mathematicians and engineers. How are we beginning to address cancer from the perspective of the physical sciences? PMID:21850037

Microbiome Tools for Forensic Science.

PubMed

Metcalf, Jessica L; Xu, Zhenjiang Z; Bouslimani, Amina; Dorrestein, Pieter; Carter, David O; Knight, Rob

2017-09-01

Microbes are present at every crime scene and have been used as physical evidence for over a century. Advances in DNA sequencing and computational approaches have led to recent breakthroughs in the use of microbiome approaches for forensic science, particularly in the areas of estimating postmortem intervals (PMIs), locating clandestine graves, and obtaining soil and skin trace evidence. Low-cost, high-throughput technologies allow us to accumulate molecular data quickly and to apply sophisticated machine-learning algorithms, building generalizable predictive models that will be useful in the criminal justice system. In particular, integrating microbiome and metabolomic data has excellent potential to advance microbial forensics. Copyright © 2017. Published by Elsevier Ltd.

AACR precision medicine series: Highlights of the integrating clinical genomics and cancer therapy meeting.

PubMed

Maggi, Elaine; Montagna, Cristina

2015-12-01

The American Association for Cancer Research (AACR) Precision Medicine Series "Integrating Clinical Genomics and Cancer Therapy" took place June 13-16, 2015 in Salt Lake City, Utah. The conference was co-chaired by Charles L. Sawyers form Memorial Sloan Kettering Cancer Center in New York, Elaine R. Mardis form Washington University School of Medicine in St. Louis, and Arul M. Chinnaiyan from University of Michigan in Ann Arbor. About 500 clinicians, basic science investigators, bioinformaticians, and postdoctoral fellows joined together to discuss the current state of Clinical Genomics and the advances and challenges of integrating Next Generation Sequencing (NGS) technologies into clinical practice. The plenary sessions and panel discussions covered current platforms and sequencing approaches adopted for NGS assays of cancer genome at several national and international institutions, different approaches used to map and classify targetable sequence variants, and how information acquired with the sequencing of the cancer genome is used to guide treatment options. While challenges still exist from a technological perspective, it emerged that there exists considerable need for the development of tools to aid the identification of the therapy most suitable based on the mutational profile of the somatic cancer genome. The process to match patients to ongoing clinical trials is still complex. In addition, the need for centralized data repositories, preferably linked to well annotated clinical records, that aid sharing of sequencing information is central to begin understanding the contribution of variants of unknown significance to tumor etiology and response to therapy. Here we summarize the highlights of this stimulating four-day conference with a major emphasis on the open problems that the clinical genomics community is currently facing and the tools most needed for advancing this field. Copyright © 2015. Published by Elsevier B.V. All rights reserved.

UTeach: Secondary Teacher Preparation in Science and Mathematics at the University of Texas at Austin

NASA Astrophysics Data System (ADS)

Marder, Michael

2006-03-01

The UTeach Program is a joint effort of the College of Natural Sciences, the College of Education and the Austin Independent School District to recruit, prepare and support math and science teachers for the State of Texas. UTeach uses early and on-going field experiences to capture the imagination of preservice teachers and provide a foundation for more advanced pedagogical courses. With over 400 students enrolled and over 80 graduates per year, UTeach is one of the largest programs producing secondary science, mathematics, and computer science teachers in the nation. Most UTeach students are undergraduates, but around 10% are people of many ages with strong backgrounds in mathematics or science who have decided to enter teaching. Hallmarks include: *Four-year degree plans that enable undergraduates to obtain certification at no cost in time or money. *Active recruitment and support including tuition reimbursement, paid internships, personal advising, and guidance by master teachers. *Emphasis on preparing teachers who will be knowledgeable of their discipline, experienced with involving students in scientific inquiry, and practiced in employing new technologies to enhance student learning. *A revised, streamlined professional education sequence drawing on research on learning, standards-based curricula, multiple forms of assessment, and proven strategies for achieving equity and integrating technology into math and science education. *Program flexibility with multiple entry points (from freshman to post baccalaureate), integrated degree plans, and proficiency-based assessment, including the development of individual teaching portfolios. For more information on UTeach, see http://uteach.utexas.edu

Design of Mariner 9 Science Sequences using Interactive Graphics Software

NASA Technical Reports Server (NTRS)

Freeman, J. E.; Sturms, F. M, Jr.; Webb, W. A.

1973-01-01

This paper discusses the analyst/computer system used to design the daily science sequences required to carry out the desired Mariner 9 science plan. The Mariner 9 computer environment, the development and capabilities of the science sequence design software, and the techniques followed in the daily mission operations are discussed. Included is a discussion of the overall mission operations organization and the individual components which played an essential role in the sequence design process. A summary of actual sequences processed, a discussion of problems encountered, and recommendations for future applications are given.

ADOMA: A Command Line Tool to Modify ClustalW Multiple Alignment Output.

PubMed

Zaal, Dionne; Nota, Benjamin

2016-01-01

We present ADOMA, a command line tool that produces alternative outputs from ClustalW multiple alignments of nucleotide or protein sequences. ADOMA can simplify the output of alignments by showing only the different residues between sequences, which is often desirable when only small differences such as single nucleotide polymorphisms are present (e.g., between different alleles). Another feature of ADOMA is that it can enhance the ClustalW output by coloring the residues in the alignment. This tool is easily integrated into automated Linux pipelines for next-generation sequencing data analysis, and may be useful for researchers in a broad range of scientific disciplines including evolutionary biology and biomedical sciences. The source code is freely available at https://sourceforge. net/projects/adoma/. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Reflections on Communicating Science during the Canterbury Earthquake Sequence of 2010-2011, New Zealand

NASA Astrophysics Data System (ADS)

Wein, A. M.; Berryman, K. R.; Jolly, G. E.; Brackley, H. L.; Gledhill, K. R.

2015-12-01

The 2010-2011 Canterbury Earthquake Sequence began with the 4th September 2010 Darfield earthquake (Mw 7.1). Perhaps because there were no deaths, the mood of the city and the government was that high standards of earthquake engineering in New Zealand protected us, and there was a confident attitude to response and recovery. The demand for science and engineering information was of interest but not seen as crucial to policy, business or the public. The 22nd February 2011 Christchurch earthquake (Mw 6.2) changed all that; there was a significant death toll and many injuries. There was widespread collapse of older unreinforced and two relatively modern multi-storey buildings, and major disruption to infrastructure. The contrast in the interest and relevance of the science could not have been greater compared to 5 months previously. Magnitude 5+ aftershocks over a 20 month period resulted in confusion, stress, an inability to define a recovery trajectory, major concerns about whether insurers and reinsurers would continue to provide cover, very high levels of media interest from New Zealand and around the world, and high levels of political risk. As the aftershocks continued there was widespread speculation as to what the future held. During the sequence, the science and engineering sector sought to coordinate and offer timely and integrated advice. However, other than GeoNet, the national geophysical monitoring network, there were few resources devoted to communication, with the result that it was almost always reactive. With hindsight we have identified the need to resource information gathering and synthesis, execute strategic assessments of stakeholder needs, undertake proactive communication, and develop specific information packages for the diversity of users. Overall this means substantially increased resources. Planning is now underway for the science sector to adopt the New Zealand standardised CIMS (Coordinated Incident Management System) structure for management and communication during a crisis, which should help structure and resource the science response needs in future major events.

Communicating the Benefits of a Full Sequence of High School Science Courses

NASA Astrophysics Data System (ADS)

Nicholas, Catherine Marie

High school students are generally uninformed about the benefits of enrolling in a full sequence of science courses, therefore only about a third of our nation's high school graduates have completed the science sequence of Biology, Chemistry and Physics. The lack of students completing a full sequence of science courses contributes to the deficit in the STEM degree production rate needed to fill the demand of the current job market and remain competitive as a nation. The purpose of the study was to make a difference in the number of students who have access to information about the benefits of completing a full sequence of science courses. This dissertation study employed qualitative research methodology to gain a broad perspective of staff through a questionnaire and document review and then a deeper understanding through semi-structured interview protocol. The data revealed that a universal sequence of science courses in the high school district did not exist. It also showed that not all students had access to all science courses; students were sorted and tracked according to prerequisites that did not necessarily match the skill set needed for the courses. In addition, the study showed a desire for more support and direction from the district office. It was also apparent that there was a disconnect that existed between who staff members believed should enroll in a full sequence of science courses and who actually enrolled. Finally, communication about science was shown to occur mainly through counseling and peers. A common science sequence, detracking of science courses, increased communication about the postsecondary and academic benefits of a science education, increased district direction and realistic mathematics alignment were all discussed as solutions to the problem.

An investigation of the impact of science course sequencing on student performance in high school science and math

NASA Astrophysics Data System (ADS)

Mary, Michael Todd

High school students in the United States for the past century have typically taken science courses in a sequence of biology followed by chemistry and concluding with physics. An alternative sequence, typically referred to as "physics first" inverts the traditional sequence by having students begin with physics and end with biology. Proponents of physics first cite advances in biological sciences that have dramatically changed the nature of high school biology and the potential benefit to student learning in math that would accompany taking an algebra-based physics course in the early years of high school to support changing the sequence. Using a quasi-experimental, quantitative research design, the purpose of this study was to investigate the impact of science course sequencing on student achievement in math and science at a school district that offered both course sequences. The Texas state end-of-course exams in biology, chemistry, physics, algebra I and geometry were used as the instruments measuring student achievement in math and science at the end of each academic year. Various statistical models were used to analyze these achievement data. The conclusion was, for students in this study, the sequence in which students took biology, chemistry, and physics had little or no impact on performance on the end-of-course assessments in each of these courses. Additionally there was only a minimal effect found with respect to math performance, leading to the conclusion that neither the traditional or "physics first" science course sequence presented an advantage for student achievement in math or science.

Spatial Based Integrated Assessment of Bedrock and Ground Motions, Fault Offsets, and Their Effects for the October-November 2002 Earthquake Sequence on the Denali Fault, Alaska

NASA Astrophysics Data System (ADS)

Vinson, T. S.; Carlson, R.; Hansen, R.; Hulsey, L.; Ma, J.; White, D.; Barnes, D.; Shur, Y.

2003-12-01

A National Science Foundation (NSF) Small Grant Exploratory Research Grant was awarded to the University of Alaska Fairbanks to archive bedrock and ground motions and fault offsets and their effects for the October-November 2002 earthquake sequence on the Denali Fault, Alaska. The scope of work included the accumulation of all strong motion records, satellite imagery, satellite remote sensing data, aerial and ground photographs, and structural response (both measured and anecdotal) that would be useful to achieve the objective. Several interesting data sets were archived including ice cover, lateral movement of stream channels, landslides, avalanches, glacial fracturing, "felt" ground motions, and changes in water quantity and quality. The data sources may be spatially integrated to provide a comprehensive assessment of the bedrock and ground motions and fault offsets for the October-November 2002 earthquake sequence. In the aftermath of the October-November 2002 earthquake sequence on the Denali fault, the Alaskan engineering community expressed a strong interest to understand why their structures and infrastructure were not substantially damaged by the ground motions they experienced during the October-November 2002 Earthquake Sequence on the Denali Fault. The research work proposed under this NSF Grant is a necessary prerequisite to this understanding. Furthermore, the proposed work will facilitate a comparison of Denali events with the Loma Prieta and recent Kocelli and Dozce events in Turkey, all of which were associated with strike-slip faulting. Finally, the spatially integrated data will provide the basis for research work that is truly innovative. For example, is may be possible to predict the observed (1) landsliding and avalanches, (2) changes in water quantity and quality, (3) glacial fracturing, and (4) the widespread liquefaction and lateral spreading, which occurred along the Tok cutoff and Northway airport, with the bedrock and ground motions and fault offsets extrapolated from the product of the research. An integrated assessment of the composite effects may be performed to better understand the bedrock and ground motions and fault offset regime that existed during the earthquake sequence.

Evaluation of a Secondary School Science Program Inversion: Moving from a Traditional to a Modifified-PCB Sequence

ERIC Educational Resources Information Center

Gaubatz, Julie

2013-01-01

Studies of high-school science course sequences have been limited primarily to a small number of site-specific investigations comparing traditional science sequences (e.g., Biology-Chemistry-Physics: BCP) to various Physics First-influenced sequences (Physics-Chemistry-Biology: PCB). The present study summarizes a five-year program evaluation…

Mass spectrometry-based protein identification by integrating de novo sequencing with database searching.

PubMed

Wang, Penghao; Wilson, Susan R

2013-01-01

Mass spectrometry-based protein identification is a very challenging task. The main identification approaches include de novo sequencing and database searching. Both approaches have shortcomings, so an integrative approach has been developed. The integrative approach firstly infers partial peptide sequences, known as tags, directly from tandem spectra through de novo sequencing, and then puts these sequences into a database search to see if a close peptide match can be found. However the current implementation of this integrative approach has several limitations. Firstly, simplistic de novo sequencing is applied and only very short sequence tags are used. Secondly, most integrative methods apply an algorithm similar to BLAST to search for exact sequence matches and do not accommodate sequence errors well. Thirdly, by applying these methods the integrated de novo sequencing makes a limited contribution to the scoring model which is still largely based on database searching. We have developed a new integrative protein identification method which can integrate de novo sequencing more efficiently into database searching. Evaluated on large real datasets, our method outperforms popular identification methods.

Genome Sequencing Technologies and Nursing: What Are the Roles of Nurses and Nurse Scientists?

PubMed

Taylor, Jacquelyn Y; Wright, Michelle L; Hickey, Kathleen T; Housman, David E

Advances in DNA sequencing technology have resulted in an abundance of personalized data with challenging clinical utility and meaning for clinicians. This wealth of data has potential to dramatically impact the quality of healthcare. Nurses are at the focal point in educating patients regarding relevant healthcare needs; therefore, an understanding of sequencing technology and utilizing these data are critical. The objective of this study was to explicate the role of nurses and nurse scientists as integral members of healthcare teams in improving understanding of DNA sequencing data and translational genomics for patients. A history of the nurse role in newborn screening is used as an exemplar. This study serves as an exemplar on how genome sequencing has been utilized in nursing science and incorporates linkages of other omics approaches used by nurses that are included in this special issue. This special issue showcased nurse scientists conducting multi-omic research from various methods, including targeted candidate genes, pharmacogenomics, proteomics, epigenomics, and the microbiome. From this vantage point, we provide an overview of the roles of nurse scientists in genome sequencing research and provide recommendations for the best utilization of nurses and nurse scientists related to genome sequencing.

Brain Region-Specific Expression of Genes Mapped within Quantitative Trait Loci for Behavioral Responsiveness to Acute Stress in Fisher 344 and Wistar Kyoto Male Rats (Postprint)

DTIC Science & Technology

2018-03-12

Integrative Genomics Viewer (Broad Institute, Cambridge, Massachusetts), we iden- tified the coding sequence variations between the F344 and WKY... abnormalities and disturbances in brain metabolism resem- bling those in depressive states [74]. Ifna2 is also known to induce memory, concentration, and...Variant and Chronic Interpersonal Stress Prospectively Predicts Social Anxiety and Depression Symptoms Over Six Years. Clinical psychological science

GAMES identifies and annotates mutations in next-generation sequencing projects.

PubMed

Sana, Maria Elena; Iascone, Maria; Marchetti, Daniela; Palatini, Jeff; Galasso, Marco; Volinia, Stefano

2011-01-01

Next-generation sequencing (NGS) methods have the potential for changing the landscape of biomedical science, but at the same time pose several problems in analysis and interpretation. Currently, there are many commercial and public software packages that analyze NGS data. However, the limitations of these applications include output which is insufficiently annotated and of difficult functional comprehension to end users. We developed GAMES (Genomic Analysis of Mutations Extracted by Sequencing), a pipeline aiming to serve as an efficient middleman between data deluge and investigators. GAMES attains multiple levels of filtering and annotation, such as aligning the reads to a reference genome, performing quality control and mutational analysis, integrating results with genome annotations and sorting each mismatch/deletion according to a range of parameters. Variations are matched to known polymorphisms. The prediction of functional mutations is achieved by using different approaches. Overall GAMES enables an effective complexity reduction in large-scale DNA-sequencing projects. GAMES is available free of charge to academic users and may be obtained from http://aqua.unife.it/GAMES.

Preparing Historically Underserved Students for STEM Careers: The Role of an Inquiry-based High School Science Sequence Beginning with Physics

NASA Astrophysics Data System (ADS)

Bridges, Jon P.

Improving the STEM readiness of students from historically underserved groups is a moral and economic imperative requiring greater attention and effort than has been shown to date. The current literature suggests a high school science sequence beginning with physics and centered on developing conceptual understanding, using inquiry labs and modeling to allow students to explore new ideas, and addressing and correcting student misconceptions can increase student interest in and preparation for STEM careers. The purpose of this study was to determine if the science college readiness of historically underserved students can be improved by implementing an inquiry-based high school science sequence comprised of coursework in physics, chemistry, and biology for every student. The study used a retrospective cohort observational design to address the primary research question: are there differences between historically underserved students completing a Physics First science sequence and their peers completing a traditional science sequence in 1) science college-readiness test scores, 2) rates of science college-and career-readiness, and 3) interest in STEM? Small positive effects were found for all three outcomes for historically underserved students in the Physics First sequence.

Fueling the Future with Fungal Genomes

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

Grigoriev, Igor V.

2014-10-27

Genomes of fungi relevant to energy and environment are in focus of the JGI Fungal Genomic Program. One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts and pathogens) and biorefinery processes (cellulose degradation and sugar fermentation) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Science Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 400 fungal genomes have beenmore » sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics will lead to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such ‘parts’ suggested by comparative genomics and functional analysis in these areas are presented here.« less

DNA Data Bank of Japan

PubMed Central

Mashima, Jun; Kodama, Yuichi; Fujisawa, Takatomo; Katayama, Toshiaki; Okuda, Yoshihiro; Kaminuma, Eli; Ogasawara, Osamu; Okubo, Kousaku; Nakamura, Yasukazu; Takagi, Toshihisa

2017-01-01

The DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) has been providing public data services for thirty years (since 1987). We are collecting nucleotide sequence data from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org), in collaboration with the US National Center for Biotechnology Information (NCBI) and European Bioinformatics Institute (EBI). The DDBJ Center also services Japanese Genotype-phenotype Archive (JGA), with the National Bioscience Database Center to collect human-subjected data from Japanese researchers. Here, we report our database activities for INSDC and JGA over the past year, and introduce retrieval and analytical services running on our supercomputer system and their recent modifications. Furthermore, with the Database Center for Life Science, the DDBJ Center improves semantic web technologies to integrate and to share biological data, for providing the RDF version of the sequence data. PMID:27924010

Students' communication, argumentation and knowledge in a citizens' conference on global warming

NASA Astrophysics Data System (ADS)

Albe, Virginie; Gombert, Marie-José

2012-09-01

An empirical study on 12th-grade students' engagement on a global warming debate as a citizens' conference is reported. Within the design-based research methodology, an interdisciplinary teaching sequence integrating an initiation to non-violent communication was developed. Students' debates were analyzed according to three dimensions: communication, argumentation, and knowledge. Students regulated their oral contributions to the debate by identifying judgments in their discussions. Rhetorical processes developed by students were mainly related to the identity of debate protagonists with interest attributions, authority, and positions. Students' arguments also relied on empirical data. The students' knowledge focused on energy choices, economic, political, and science development issues. Implications for socioscientific issues integration in class are discussed.

Chemistry, the Central Science? The History of the High School Science Sequence

ERIC Educational Resources Information Center

Sheppard, Keith; Robbins, Dennis M.

2005-01-01

Chemistry became the ''central science'' not by design but by accident in the US high schools. The three important factors, which had their influence on the high school science, are sequenced and their impact on the development of US science education, are mentioned.

Defining Genome Project Standards in a New Era of Sequencing (GSC8 Meeting)

ScienceCinema

Chain, Patrick

2018-01-15

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego.

The Sequencing of Basic Chemistry Topics by Physical Science Teachers

ERIC Educational Resources Information Center

Sibanda, Doras; Hobden, Paul

2016-01-01

The purpose of this study was to find out teachers' preferred teaching sequence for basic chemistry topics in Physical Science in South Africa, to obtain their reasons underpinning their preferred sequence, and to compare these sequences with the prescribed sequences in the current curriculum. The study was located within a pragmatic paradigm and…

VISA--Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing.

PubMed

Hocum, Jonah D; Battrell, Logan R; Maynard, Ryan; Adair, Jennifer E; Beard, Brian C; Rawlings, David J; Kiem, Hans-Peter; Miller, Daniel G; Trobridge, Grant D

2015-07-07

Analyzing the integration profile of retroviral vectors is a vital step in determining their potential genotoxic effects and developing safer vectors for therapeutic use. Identifying retroviral vector integration sites is also important for retroviral mutagenesis screens. We developed VISA, a vector integration site analysis server, to analyze next-generation sequencing data for retroviral vector integration sites. Sequence reads that contain a provirus are mapped to the human genome, sequence reads that cannot be localized to a unique location in the genome are filtered out, and then unique retroviral vector integration sites are determined based on the alignment scores of the remaining sequence reads. VISA offers a simple web interface to upload sequence files and results are returned in a concise tabular format to allow rapid analysis of retroviral vector integration sites.

Genome Sequencing Technologies and Nursing: What Are the Roles of Nurses and Nurse Scientists?

PubMed Central

Taylor, Jacquelyn Y.; Wright, Michelle L.; Hickey, Kathleen T.; Housman, David

2016-01-01

Background Advances in DNA sequencing technology have resulted in an abundance of personalized data with challenging clinical utility and meaning for clinicians. This wealth of data has potential to dramatically impact the quality of healthcare. Nurses are at the focal point in educating patients regarding relevant healthcare needs; therefore, an understanding of sequencing technology and utilizing these data are critical. Aim The objective of this paper is to explicate the role of nurses and nurse scientists as integral members of healthcare teams in improving understanding of DNA sequencing data and translational genomics for patients. Approach A history of the nurse role in newborn screening is used as an exemplar. Discussion This paper serves as an exemplar on how genome sequencing has been utilized in nursing science and incorporates linkages of other omics approaches used by nurses that are included in this special issue. This special issue showcased nurse scientists conducting multi-omic research from various methods, including targeted candidate genes, pharmacogenomics, proteomics, epigenomics and the microbiome. From this vantage point, we provide an overview of the roles of nurse scientists in genome sequencing research and provide recommendations for the best utilization of nurses and nurse scientists related to genome sequencing. PMID:28252579

Calculating the quality of public high-throughput sequencing data to obtain a suitable subset for reanalysis from the Sequence Read Archive

PubMed Central

Nakazato, Takeru; Bono, Hidemasa

2017-01-01

Abstract It is important for public data repositories to promote the reuse of archived data. In the growing field of omics science, however, the increasing number of submissions of high-throughput sequencing (HTSeq) data to public repositories prevents users from choosing a suitable data set from among the large number of search results. Repository users need to be able to set a threshold to reduce the number of results to obtain a suitable subset of high-quality data for reanalysis. We calculated the quality of sequencing data archived in a public data repository, the Sequence Read Archive (SRA), by using the quality control software FastQC. We obtained quality values for 1 171 313 experiments, which can be used to evaluate the suitability of data for reuse. We also visualized the data distribution in SRA by integrating the quality information and metadata of experiments and samples. We provide quality information of all of the archived sequencing data, which enable users to obtain sufficient quality sequencing data for reanalyses. The calculated quality data are available to the public in various formats. Our data also provide an example of enhancing the reuse of public data by adding metadata to published research data by a third party. PMID:28449062

Minitrack on data and knowledge base issues in genomics at the 27th Hawaii International Conference on system sciences

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

NONE

1995-05-01

This report is a summary of the proceedings from the Minitrack on Data and Knowledge Base Issues in Genomics at the 27th Hawaii International Conference on System Science, January 4 - 7, 1994. The minitrack was organized by Dong-Guk Shin (University of Connecticut) and Francois Rechenmann (INRIA, France). Support was jointly provided by the NSF, NIH and DOE. The minitrack included, after rigorous review, ten full papers and four extended abstracts in the following five different research subareas of genome informatics: data modeling and management, sequence analysis, graphical user interface, interoperation in a heterogenous computing environment, and system integration inmore » a knowledge-based approach.« less

Encapsulins: microbial nanocompartments with applications in biomedicine, nanobiotechnology and materials science.

PubMed

Giessen, Tobias W

2016-10-01

Compartmentalization is one of the defining features of life. Cells use protein compartments to exert spatial control over their metabolism, store nutrients and create unique microenvironments needed for essential physiological processes. Encapsulins are a recently discovered class of protein nanocompartments found in bacteria and archaea that naturally encapsulate cargo proteins. A short C-terminal targeting sequence directs the highly specific encapsulation process in vivo. Here, I will initially discuss the properties, diversity and putative function of encapsulins. The unique characteristics and potential uses of the self-sorting cargo-packaging process found in encapsulin systems will then be highlighted. Examples for the application of encapsulins as cell-specific optical nanoprobes and targeted therapeutic delivery systems will be discussed with an emphasis on the ability to integrate multiple functionalities within a single nanodevice. By fusing targeting sequences to non-native proteins, encapsulins can also be used as specific nanocontainers and enzymatic nanoreactors in vivo. I will end by briefly discussing future avenues for encapsulin research related to both basic microbial metabolism and applications in biomedicine, catalysis and materials science. Copyright © 2016 Elsevier Ltd. All rights reserved.

Development of a NASA 2018 Mars Landed Mission Concept

NASA Technical Reports Server (NTRS)

Wilson, M. G.; Salvo, C. G.; Abilleira, F.; Sengstacken, A. J.; Allwood, A. G.; Backes, P. G.; Lindemann, R. A.; Jordan, J. F.

2010-01-01

Fundamental to NASA's Mars Exploration Program (MEP) is an ongoing development of an integrated and coordinated set of possible future candidate missions that meet fundamental science and programmatic objectives of NASA and the Mars scientific community. In the current planning horizon of the NASA MEP, a landed mobile surface exploration mission launching in the 2018 Mars launch opportunity exists as a candidate project to meet MEP in situ science and exploration objectives. This paper describes the proposed mission science objectives and the mission implementation concept developed for the 2018 opportunity. As currently envisioned, this mission concept seeks to explore a yet-to-be-selected site with high preservation potential for physical and chemical biosignatures, evaluate paleoenvironmental conditions, characterize the potential for preservation of biosignatures, and access multiple sequences of geological units in a search for evidence of past life and/or prebiotic chemistry at a site on Mars.

Middle Level SS&C Energy Series.

ERIC Educational Resources Information Center

Crow, Linda W.; Aldridge, Bill G.

The project on Scope Sequence and Coordination of Secondary School Science (SS&C) was initiated by the National Science Teachers Association (NSTA) and recommends that all students study science every year and advocates carefully sequenced, well-coordinated instruction in biology, chemistry, earth/space science, and physics. This document…

Database Resources of the BIG Data Center in 2018

PubMed Central

Xu, Xingjian; Hao, Lili; Zhu, Junwei; Tang, Bixia; Zhou, Qing; Song, Fuhai; Chen, Tingting; Zhang, Sisi; Dong, Lili; Lan, Li; Wang, Yanqing; Sang, Jian; Hao, Lili; Liang, Fang; Cao, Jiabao; Liu, Fang; Liu, Lin; Wang, Fan; Ma, Yingke; Xu, Xingjian; Zhang, Lijuan; Chen, Meili; Tian, Dongmei; Li, Cuiping; Dong, Lili; Du, Zhenglin; Yuan, Na; Zeng, Jingyao; Zhang, Zhewen; Wang, Jinyue; Shi, Shuo; Zhang, Yadong; Pan, Mengyu; Tang, Bixia; Zou, Dong; Song, Shuhui; Sang, Jian; Xia, Lin; Wang, Zhennan; Li, Man; Cao, Jiabao; Niu, Guangyi; Zhang, Yang; Sheng, Xin; Lu, Mingming; Wang, Qi; Xiao, Jingfa; Zou, Dong; Wang, Fan; Hao, Lili; Liang, Fang; Li, Mengwei; Sun, Shixiang; Zou, Dong; Li, Rujiao; Yu, Chunlei; Wang, Guangyu; Sang, Jian; Liu, Lin; Li, Mengwei; Li, Man; Niu, Guangyi; Cao, Jiabao; Sun, Shixiang; Xia, Lin; Yin, Hongyan; Zou, Dong; Xu, Xingjian; Ma, Lina; Chen, Huanxin; Sun, Yubin; Yu, Lei; Zhai, Shuang; Sun, Mingyuan; Zhang, Zhang; Zhao, Wenming; Xiao, Jingfa; Bao, Yiming; Song, Shuhui; Hao, Lili; Li, Rujiao; Ma, Lina; Sang, Jian; Wang, Yanqing; Tang, Bixia; Zou, Dong; Wang, Fan

2018-01-01

Abstract The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. PMID:29036542

The effect of curriculum changes and instructional techniques on science-reasoning skills among high school students

NASA Astrophysics Data System (ADS)

Newman, Joan T.

Any change, particularly on a large scale like a sequence change in a district with 75,000 students, is difficult. However, with the advent of the new TAKS science test and the new requirements for high school graduation in the state of Texas, educators and students alike are engaged in innovative educational approaches to meet these requirements. This study investigated a different, non-traditional science sequence to investigate relationships among secondary core-science course sequencing, student science-reasoning performance, and classroom pedagogy. The methodology adopted in the study led to a deeper understanding of the successes and challenges faced by teachers in teaching conceptual physics and chemistry to 8 th and 9th grade students. The qualitative analysis suggested a difference in pedagogy employed by middle and high school science teachers and a need for secondary science teachers to enhance their content knowledge and pedagogical skills, as well as change their underlying attitudes and beliefs about the abilities of students. The study examined scores of 495 randomly chosen students following three different matriculation patterns within one large independent school district. The study indicated that students who follow a sequence with 9th grade IPC generally increase their science-reasoning skills as demonstrated on the 10th grade TAKS science test when these scores are compared with those of students who do not have 9th grade IPC in the science sequence.

Anatomy as the Backbone of an Integrated First Year Medical Curriculum: Design and Implementation

PubMed Central

Klement, Brenda J.; Paulsen, Douglas F.; Wineski, Lawrence E

2011-01-01

Morehouse School of Medicine chose to restructure its first year medical curriculum in 2005. The anatomy faculty had prior experience in integrating courses, stemming from the successful integration of individual anatomical sciences courses into a single course called Human Morphology. The integration process was expanded to include the other first year basic science courses (Biochemistry, Physiology, and Neurobiology) as we progressed toward an integrated curriculum. A team, consisting of the course directors, a curriculum coordinator and the Associate Dean for Educational and Faculty Affairs, was assembled to build the new curriculum. For the initial phase, the original course titles were retained but the lecture order was reorganized around the Human Morphology topic sequence. The material from all four courses was organized into four sequential units. Other curricular changes included placing laboratories and lectures more consistently in the daily routine, reducing lecture time from 120 to 90 minute blocks, eliminating unnecessary duplication of content, and increasing the amount of independent study time. Examinations were constructed to include questions from all courses on a single test, reducing the number of examination days in each block from three to one. The entire restructuring process took two years to complete, and the revised curriculum was implemented for the students entering in 2007. The outcomes of the restructured curriculum include a reduction in the number of contact hours by 28%, higher or equivalent subject examination average scores, enhanced student satisfaction, and a first year curriculum team better prepared to move forward with future integration. PMID:21538939

Putting Physics First: Three Case Studies of High School Science Department and Course Sequence Reorganization

ERIC Educational Resources Information Center

Larkin, Douglas B.

2016-01-01

This article examines the process of shifting to a "Physics First" sequence in science course offerings in three school districts in the United States. This curricular sequence reverses the more common U.S. high school sequence of biology/chemistry/physics, and has gained substantial support in the physics education community over the…

The Infrastructure of an Integrated Virtual Reality Environment for International Space Welding Experiment

NASA Technical Reports Server (NTRS)

Wang, Peter Hor-Ching

1996-01-01

This study is a continuation of the summer research of 1995 NASA/ASEE Summer Faculty Fellowship Program. This effort is to provide the infrastructure of an integrated Virtual Reality (VR) environment for the International Space Welding Experiment (ISWE) Analytical Tool and Trainer and the Microgravity Science Glovebox (MSG) Analytical Tool study. Due to the unavailability of the MSG CAD files and the 3D-CAD converter, little was done to the MSG study. However, the infrastructure of the integrated VR environment for ISWE is capable of performing the MSG study when the CAD files become available. Two primary goals are established for this research. First, the essential peripheral devices for an integrated VR environment will be studied and developed for the ISWE and MSG studies. Secondly, the training of the flight crew (astronaut) in general orientation, procedures, and location, orientation, and sequencing of the welding samples and tools are built into the VR system for studying the welding process and training the astronaut.

Efficient generation of transgenic cattle using the DNA transposon and their analysis by next-generation sequencing

PubMed Central

Yum, Soo-Young; Lee, Song-Jeon; Kim, Hyun-Min; Choi, Woo-Jae; Park, Ji-Hyun; Lee, Won-Wu; Kim, Hee-Soo; Kim, Hyeong-Jong; Bae, Seong-Hun; Lee, Je-Hyeong; Moon, Joo-Yeong; Lee, Ji-Hyun; Lee, Choong-Il; Son, Bong-Jun; Song, Sang-Hoon; Ji, Su-Min; Kim, Seong-Jin; Jang, Goo

2016-01-01

Here, we efficiently generated transgenic cattle using two transposon systems (Sleeping Beauty and Piggybac) and their genomes were analyzed by next-generation sequencing (NGS). Blastocysts derived from microinjection of DNA transposons were selected and transferred into recipient cows. Nine transgenic cattle have been generated and grown-up to date without any health issues except two. Some of them expressed strong fluorescence and the transgene in the oocytes from a superovulating one were detected by PCR and sequencing. To investigate genomic variants by the transgene transposition, whole genomic DNA were analyzed by NGS. We found that preferred transposable integration (TA or TTAA) was identified in their genome. Even though multi-copies (i.e. fifteen) were confirmed, there was no significant difference in genome instabilities. In conclusion, we demonstrated that transgenic cattle using the DNA transposon system could be efficiently generated, and all those animals could be a valuable resource for agriculture and veterinary science. PMID:27324781

Distribution and clinical impact of functional variants in 50,726 whole-exome sequences from the DiscovEHR study.

PubMed

Dewey, Frederick E; Murray, Michael F; Overton, John D; Habegger, Lukas; Leader, Joseph B; Fetterolf, Samantha N; O'Dushlaine, Colm; Van Hout, Cristopher V; Staples, Jeffrey; Gonzaga-Jauregui, Claudia; Metpally, Raghu; Pendergrass, Sarah A; Giovanni, Monica A; Kirchner, H Lester; Balasubramanian, Suganthi; Abul-Husn, Noura S; Hartzel, Dustin N; Lavage, Daniel R; Kost, Korey A; Packer, Jonathan S; Lopez, Alexander E; Penn, John; Mukherjee, Semanti; Gosalia, Nehal; Kanagaraj, Manoj; Li, Alexander H; Mitnaul, Lyndon J; Adams, Lance J; Person, Thomas N; Praveen, Kavita; Marcketta, Anthony; Lebo, Matthew S; Austin-Tse, Christina A; Mason-Suares, Heather M; Bruse, Shannon; Mellis, Scott; Phillips, Robert; Stahl, Neil; Murphy, Andrew; Economides, Aris; Skelding, Kimberly A; Still, Christopher D; Elmore, James R; Borecki, Ingrid B; Yancopoulos, George D; Davis, F Daniel; Faucett, William A; Gottesman, Omri; Ritchie, Marylyn D; Shuldiner, Alan R; Reid, Jeffrey G; Ledbetter, David H; Baras, Aris; Carey, David J

2016-12-23

The DiscovEHR collaboration between the Regeneron Genetics Center and Geisinger Health System couples high-throughput sequencing to an integrated health care system using longitudinal electronic health records (EHRs). We sequenced the exomes of 50,726 adult participants in the DiscovEHR study to identify ~4.2 million rare single-nucleotide variants and insertion/deletion events, of which ~176,000 are predicted to result in a loss of gene function. Linking these data to EHR-derived clinical phenotypes, we find clinical associations supporting therapeutic targets, including genes encoding drug targets for lipid lowering, and identify previously unidentified rare alleles associated with lipid levels and other blood level traits. About 3.5% of individuals harbor deleterious variants in 76 clinically actionable genes. The DiscovEHR data set provides a blueprint for large-scale precision medicine initiatives and genomics-guided therapeutic discovery. Copyright © 2016, American Association for the Advancement of Science.

Super-resolution optical imaging and magnetometry using NV centers in diamond

NASA Astrophysics Data System (ADS)

Jaskula, Jean-Christophe; Trifonov, Alexei; Glenn, David; Bar-Gill, Nir; Walsworth, Ronald

2013-05-01

We report progress done on the development and application of depletion-based techniques for super-resolution (nanoscale) optical imaging and magnetometry using NV centers in diamond. In particulare we are integrating stimulated emission depletion (STED) and ground state depletion (GSD) imaging techniques with advanced pulsed sequences for AC magnetometry. NV centers in diamond do not bleach under optical excitation, have long-lived electronic spin coherence and spin-state-dependent fluorescence, and are not biotoxic. Thus NV-diamond has great potential in quantum science and as a nanoscale magnetic biosensor.

Scope and Sequence. Life Sciences, Physical Sciences, Earth and Space Sciences. A Summer Curriculum Development Project.

ERIC Educational Resources Information Center

Cortland-Madison Board of Cooperative Educational Services, Cortland, NY.

Presented is a booklet containing scope and sequence charts for kindergarten and grades 1 to 6 science units. Overviews and lists of major concepts for units in the life, physical, and earth/space sciences are provided in tables for each grade level. Also presented are seven complete units, one for each grade level. Following a table of contents,…

An overview of human genetic privacy.

PubMed

Shi, Xinghua; Wu, Xintao

2017-01-01

The study of human genomics is becoming a Big Data science, owing to recent biotechnological advances leading to availability of millions of personal genome sequences, which can be combined with biometric measurements from mobile apps and fitness trackers, and of human behavior data monitored from mobile devices and social media. With increasing research opportunities for integrative genomic studies through data sharing, genetic privacy emerges as a legitimate yet challenging concern that needs to be carefully addressed, not only for individuals but also for their families. In this paper, we present potential genetic privacy risks and relevant ethics and regulations for sharing and protecting human genomics data. We also describe the techniques for protecting human genetic privacy from three broad perspectives: controlled access, differential privacy, and cryptographic solutions. © 2016 New York Academy of Sciences.

The Impact of Agricultural Science Education on Performance in a Biology Course

NASA Astrophysics Data System (ADS)

Ernest, Byron L.

The lack of student achievement in science is often cited in U.S. educational reports. At the study site, low student achievement in science has been an ongoing concern for administrators. The purpose of this mixed methods study was to investigate the impact of agricultural science education on student performance in a Biology course. Vygotsky's constructivist theory and Gardner's multiple intelligences theory provided the framework for the study. The quantitative research question examined the relationship between the completion of Fundamentals of Agriculture Science and Business course and student performance in Biology I. Teacher perceptions and experiences regarding the integration of science and agricultural curriculum and traditional science curriculum were examined qualitatively. A sequential explanatory design was employed using 3 years of data collected from 486 high school students and interviews with 10 teachers. Point-biserial correlation and chi square tests revealed statistically significant relationships between whether or not students completed Fundamentals of Agriculture Science and Business and Biology I course performance, as measured by the end of course assessment and the course grade. In the qualitative sequence, typological and inductive data analyses were applied to the interview data, and themes of student impact and teacher experience emerged. Social change implications may be possible through improved science education for students in this program. Agriculture science courses may be used to facilitate learning of complex science concepts, designing teacher collaboration and professional development for teaching science in a relevant context, and resultant improved student performance in science.

Next generation sequencing (NGS): a golden tool in forensic toolkit.

PubMed

Aly, S M; Sabri, D M

The DNA analysis is a cornerstone in contemporary forensic sciences. DNA sequencing technologies are powerful tools that enrich molecular sciences in the past based on Sanger sequencing and continue to glowing these sciences based on Next generation sequencing (NGS). Next generation sequencing has excellent potential to flourish and increase the molecular applications in forensic sciences by jumping over the pitfalls of the conventional method of sequencing. The main advantages of NGS compared to conventional method that it utilizes simultaneously a large number of genetic markers with high-resolution of genetic data. These advantages will help in solving several challenges such as mixture analysis and dealing with minute degraded samples. Based on these new technologies, many markers could be examined to get important biological data such as age, geographical origins, tissue type determination, external visible traits and monozygotic twins identification. It also could get data related to microbes, insects, plants and soil which are of great medico-legal importance. Despite the dozens of forensic research involving NGS, there are requirements before using this technology routinely in forensic cases. Thus, there is a great need to more studies that address robustness of these techniques. Therefore, this work highlights the applications of forensic sciences in the era of massively parallel sequencing.

Integration of Temporal and Ordinal Information During Serial Interception Sequence Learning

PubMed Central

Gobel, Eric W.; Sanchez, Daniel J.; Reber, Paul J.

2011-01-01

The expression of expert motor skills typically involves learning to perform a precisely timed sequence of movements (e.g., language production, music performance, athletic skills). Research examining incidental sequence learning has previously relied on a perceptually-cued task that gives participants exposure to repeating motor sequences but does not require timing of responses for accuracy. Using a novel perceptual-motor sequence learning task, learning a precisely timed cued sequence of motor actions is shown to occur without explicit instruction. Participants learned a repeating sequence through practice and showed sequence-specific knowledge via a performance decrement when switched to an unfamiliar sequence. In a second experiment, the integration of representation of action order and timing sequence knowledge was examined. When either action order or timing sequence information was selectively disrupted, performance was reduced to levels similar to completely novel sequences. Unlike prior sequence-learning research that has found timing information to be secondary to learning action sequences, when the task demands require accurate action and timing information, an integrated representation of these types of information is acquired. These results provide the first evidence for incidental learning of fully integrated action and timing sequence information in the absence of an independent representation of action order, and suggest that this integrative mechanism may play a material role in the acquisition of complex motor skills. PMID:21417511

Calculating the quality of public high-throughput sequencing data to obtain a suitable subset for reanalysis from the Sequence Read Archive.

PubMed

Ohta, Tazro; Nakazato, Takeru; Bono, Hidemasa

2017-06-01

It is important for public data repositories to promote the reuse of archived data. In the growing field of omics science, however, the increasing number of submissions of high-throughput sequencing (HTSeq) data to public repositories prevents users from choosing a suitable data set from among the large number of search results. Repository users need to be able to set a threshold to reduce the number of results to obtain a suitable subset of high-quality data for reanalysis. We calculated the quality of sequencing data archived in a public data repository, the Sequence Read Archive (SRA), by using the quality control software FastQC. We obtained quality values for 1 171 313 experiments, which can be used to evaluate the suitability of data for reuse. We also visualized the data distribution in SRA by integrating the quality information and metadata of experiments and samples. We provide quality information of all of the archived sequencing data, which enable users to obtain sufficient quality sequencing data for reanalyses. The calculated quality data are available to the public in various formats. Our data also provide an example of enhancing the reuse of public data by adding metadata to published research data by a third party. © The Authors 2017. Published by Oxford University Press.

Integrating the Fenton's Process with Biofiltration by to Reduce Chemical Oxygen Demand of Winery Effluents.

PubMed

Pipolo, Marco; Martins, Rui C; Quinta-Ferreira, Rosa M; Costa, Raquel

2017-03-01

The discharge of poorly decontaminated winery wastewater remains a serious environmental problem in many regions, and the industry is welcoming improved treatment methods. Here, an innovative decontamination approach integrating Fenton's process with biofiltration by Asian clams is proposed. The potential of this approach was assessed at the pilot scale using real effluent and by taking an actual industrial treatment system as a benchmark. Fenton peroxidation was observed to remove 84% of the effluent's chemical oxygen demand (COD), reducing it to 205 mg L. Subsequent biofiltration decreased the effluent's COD to approximately zero, well below the legal discharge limit of 150 mg L, in just 3 d. The reduction of the effluent's organic load through Fenton's process did not decrease its toxicity toward , but the effluent was much less harmful after biofiltration. The performance of the treatment proposed exceeded that of the integrated Fenton's process-sequencing batch reactor design implemented in the winery practice, where a residence time of around 10 d in the biological step typically results in 80 to 90% of COD removal. The method proposed is effective and compatible with typical winery budgets and potentially contributes to the management of a nuisance species. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Ocean Sciences Sequence for Grades 6-8: Climate Change Curriculum Developed Through a Collaboration Between Scientists and Educators

NASA Astrophysics Data System (ADS)

Weiss, E.; Skene, J.; Tran, L.

2011-12-01

Today's youth have been tasked with the overwhelming job of addressing the world's climate future. The students who will become the scientists, policy makers, and citizens of tomorrow must gain a robust understanding of the causes and effects of climate change, as well as possible adaptation strategies. Currently, there are few high quality curricula available to teachers that address these topics in a developmentally appropriate manner. The NOAA-funded Ocean Sciences Sequence for Grades 6-8 aims to address this gap by providing teachers with scientifically accurate climate change curriculum that hits on some of the most salient points in climate science, while simultaneously developing students' science process skills. The Ocean Sciences Sequence for Grades 6-8 is developed through a collaboration between some of the nation's leading ocean and climate scientists and the Lawrence Hall of Science's highly qualified GEMS (Great Explorations in Math & Science) curriculum development team. Scientists are active partners throughout the whole development process, from initial brainstorming of key concepts and creating the conceptual storyline for the curriculum to final review of the content and activities. As with all GEMS Sequences, the Ocean Sciences Sequence for Grades 6-8 is designed to provide significant scientific and educational depth, systematic assessments and informational readings, and incorporate new learning technologies. The goal is to focus strategically and effectively on the core concepts within ocean and climate sciences that students need to understand. This curriculum is designed in accordance with the latest research from the learning sciences, and provides numerous opportunities for students to develop inquiry skills and abilities as they learn about the practice of science through hands-on activities. The Ocean Sciences Sequence for Grades 6-8 addresses in depth a significant number of national, state, and district standards and benchmarks. It aligns with the Ocean Literacy and Climate Literacy Frameworks, as well as multiple core ideas in the new National Academy of Sciences Framework for K-12 Science Education. In brief, the curriculum comprises 33 45-minute sessions organized into three thematic units that are each driven by an exploratory question: Unit 1 (11 sessions)-How do the ocean and atmosphere interact?; Unit 2 (8 sessions)-How does carbon flow through the ocean, land, and atmosphere?; and Unit 3 (12 sessions)-What are the causes and effects of climate change? The curriculum deliberately explores the ocean and climate as global systems, and challenges students to use scientific evidence to make explanations about climate change. The Ocean Sciences Sequence for Grades 6-8 is currently being classroom tested by teachers across the United States in a wide variety of classroom settings. Evaluation is also being undertaken to determine the efficacy of the sequence in addressing the curriculum's learning goals.

The study of middle school mathematics and science teachers' practices, perceptions, and attitudes related to mathematics and science integration

NASA Astrophysics Data System (ADS)

Leszczynski, Eliza

The purpose of this qualitative study was to investigate the nature of mathematics and science connections made by sixth and seventh grade mathematics and science teachers in their classrooms. This study also examined the extent to which these connections represented mathematics and science integration and described the teachers' perceptions of and attitudes about mathematics and science integration. The primary data sources included classroom observations and teacher interviews. Findings suggested that teacher practices in making mathematics and science connections in the classroom incorporated many of the characteristics of integrated instruction presented in the literature. Teacher attitudes toward integration were found to be generally positive and supportive of integrated instruction. Mathematics teachers shared a common perception of integration being two separate lessons taught together in one lesson. In contrast, science teachers perceived integration to be a seamless blend of the two disciplines. The researcher related these perceptions and attitudes to the teachers' past experiences with mathematics and science connections and integration, and also to their practices of mathematics and science connections in the study.

Use of whole exome sequencing for the identification of Ito-based arrhythmia mechanism and therapy.

PubMed

Sturm, Amy C; Kline, Crystal F; Glynn, Patric; Johnson, Benjamin L; Curran, Jerry; Kilic, Ahmet; Higgins, Robert S D; Binkley, Philip F; Janssen, Paul M L; Weiss, Raul; Raman, Subha V; Fowler, Steven J; Priori, Silvia G; Hund, Thomas J; Carnes, Cynthia A; Mohler, Peter J

2015-05-26

Identified genetic variants are insufficient to explain all cases of inherited arrhythmia. We tested whether the integration of whole exome sequencing with well-established clinical, translational, and basic science platforms could provide rapid and novel insight into human arrhythmia pathophysiology and disease treatment. We report a proband with recurrent ventricular fibrillation, resistant to standard therapeutic interventions. Using whole-exome sequencing, we identified a variant in a previously unidentified exon of the dipeptidyl aminopeptidase-like protein-6 (DPP6) gene. This variant is the first identified coding mutation in DPP6 and augments cardiac repolarizing current (Ito) causing pathological changes in Ito and action potential morphology. We designed a therapeutic regimen incorporating dalfampridine to target Ito. Dalfampridine, approved for multiple sclerosis, normalized the ECG and reduced arrhythmia burden in the proband by >90-fold. This was combined with cilostazol to accelerate the heart rate to minimize the reverse-rate dependence of augmented Ito. We describe a novel arrhythmia mechanism and therapeutic approach to ameliorate the disease. Specifically, we identify the first coding variant of DPP6 in human ventricular fibrillation. These findings illustrate the power of genetic approaches for the elucidation and treatment of disease when carefully integrated with clinical and basic/translational research teams. © 2015 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

Site directed recombination

DOEpatents

Jurka, Jerzy W.

1997-01-01

Enhanced homologous recombination is obtained by employing a consensus sequence which has been found to be associated with integration of repeat sequences, such as Alu and ID. The consensus sequence or sequence having a single transition mutation determines one site of a double break which allows for high efficiency of integration at the site. By introducing single or double stranded DNA having the consensus sequence flanking region joined to a sequence of interest, one can reproducibly direct integration of the sequence of interest at one or a limited number of sites. In this way, specific sites can be identified and homologous recombination achieved at the site by employing a second flanking sequence associated with a sequence proximal to the 3'-nick.

Innovations in science education: infusing social emotional principles into early STEM learning

NASA Astrophysics Data System (ADS)

Garner, Pamela W.; Gabitova, Nuria; Gupta, Anuradha; Wood, Thomas

2017-10-01

We report on the development of an after-school and summer-based science, technology, engineering, and mathematics curriculum infused with the arts and social emotional learning content (STEAM SEL). Its design was motivated by theory and research that suggest that STEM education is well-suited for teaching empathy and other emotion-related skills. In this paper, we describe the activities associated with the development and design of the program and the curriculum. We provide expert-ratings of the STEAM and social emotional elements of the program and present instructor and participant feedback about the program's content and its delivery. Our results revealed that infusing the arts and social emotional learning content into science education created a holistic STEM-related curriculum that holds potential for enhancing young children's interest in and appreciation for science and its applications. The data also suggested that the program was well-developed and, generally well-executed. However, experts rated the STEAM elements of the program more positively than the SEL elements, especially with regard to sequencing of lessons and integration among the lessons and hands-on activities, indicating that program revisions are warranted.

Unusual RNA plant virus integration in the soybean genome leads to the production of small RNAs.

PubMed

da Fonseca, Guilherme Cordenonsi; de Oliveira, Luiz Felipe Valter; de Morais, Guilherme Loss; Abdelnor, Ricardo Vilela; Nepomuceno, Alexandre Lima; Waterhouse, Peter M; Farinelli, Laurent; Margis, Rogerio

2016-05-01

Horizontal gene transfer (HGT) is known to be a major force in genome evolution. The acquisition of genes from viruses by eukaryotic genomes is a well-studied example of HGT, including rare cases of non-retroviral RNA virus integration. The present study describes the integration of cucumber mosaic virus RNA-1 into soybean genome. After an initial metatranscriptomic analysis of small RNAs derived from soybean, the de novo assembly resulted a 3029-nt contig homologous to RNA-1. The integration of this sequence in the soybean genome was confirmed by DNA deep sequencing. The locus where the integration occurred harbors the full RNA-1 sequence followed by the partial sequence of an endogenous mRNA and another sequence of RNA-1 as an inverted repeat and allowing the formation of a hairpin structure. This region recombined into a retrotransposon located inside an exon of a soybean gene. The nucleotide similarity of the integrated sequence compared to other Cucumber mosaic virus sequences indicates that the integration event occurred recently. We described a rare event of non-retroviral RNA virus integration in soybean that leads to the production of a double-stranded RNA in a similar fashion to virus resistance RNAi plants. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

A quantitative study of a physics-first pilot program

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

Pasero, Spencer Lee; /Northern Illinois U.

Hundreds of high schools around the United States have inverted the traditional core sequence of high school science courses, putting physics first, followed by chemistry, and then biology. A quarter-century of theory, opinion, and anecdote are available, but the literature lacks empirical evidence of the effects of the program. The current study was designed to investigate the effects of the program on science achievement gain, growth in attitude toward science, and growth in understanding of the nature of scientific knowledge. One hundred eighty-five honor students participated in this quasi-experiment, self-selecting into either the traditional or inverted sequence. Students took themore » Explore test as freshmen, and the Plan test as sophomores. Gain scores were calculated for the composite scores and for the science and mathematics subscale scores. A two-factor analysis of variance (ANOVA) on course sequence and cohort showed significantly greater composite score gains by students taking the inverted sequence. Participants were administered surveys measuring attitude toward science and understanding of the nature of scientific knowledge twice per year. A multilevel growth model, compared across program groups, did not show any significant effect of the inverted sequence on either attitude or understanding of the nature of scientific knowledge. The sole significant parameter showed a decline in student attitude independent of course sequence toward science over the first two years of high school. The results of this study support the theory that moving physics to the front of the science sequence can improve achievement. The importance of the composite gain score on tests vertically aligned with the high-stakes ACT is discussed, and several ideas for extensions of the current study are offered.« less

Retrotransposons as regulators of gene expression.

PubMed

Elbarbary, Reyad A; Lucas, Bronwyn A; Maquat, Lynne E

2016-02-12

Transposable elements (TEs) are both a boon and a bane to eukaryotic organisms, depending on where they integrate into the genome and how their sequences function once integrated. We focus on two types of TEs: long interspersed elements (LINEs) and short interspersed elements (SINEs). LINEs and SINEs are retrotransposons; that is, they transpose via an RNA intermediate. We discuss how LINEs and SINEs have expanded in eukaryotic genomes and contribute to genome evolution. An emerging body of evidence indicates that LINEs and SINEs function to regulate gene expression by affecting chromatin structure, gene transcription, pre-mRNA processing, or aspects of mRNA metabolism. We also describe how adenosine-to-inosine editing influences SINE function and how ongoing retrotransposition is countered by the body's defense mechanisms. Copyright © 2016, American Association for the Advancement of Science.

Stable integration and expression of heterologous genes in several lactobacilli using an integration vector constructed from the integrase and attP sequences of phage ΦAT3 isolated from Lactobacillus casei ATCC 393.

PubMed

Lin, Chao-Fen; Lo, Ta-Chun; Kuo, Yang-Cheng; Lin, Thy-Hou

2013-04-01

An integration vector capable of stably integrating and maintaining in the chromosomes of several lactobacilli over hundreds of generations has been constructed. The major integration machinery used is based on the ΦAT3 integrase (int) and attP sequences determined previously. A novel core sequence located at the 3' end of the tRNA(leu) gene is identified in Lactobacillus fermentum ATCC 14931 as the integration target by the integration vector though most of such sequences found in other lactobacilli are similar to that determined previously. Due to the lack of an appropriate attB site in Lactococcus lactis MG1363, the integration vector is found to be unable to integrate into the chromosome of the strain. However, such integration can be successfully restored by cotransforming the integration vector with a replicative one harboring both attB and erythromycin resistance sequences into the strain. Furthermore, the integration vector constructed carries a promoter region of placT from the chromosome of Lactobacillus rhamnosus TCELL-1 which is used to express green fluorescence and luminance protein genes in the lactobacilli studied.

Bio and health informatics meets cloud : BioVLab as an example.

PubMed

Chae, Heejoon; Jung, Inuk; Lee, Hyungro; Marru, Suresh; Lee, Seong-Whan; Kim, Sun

2013-01-01

The exponential increase of genomic data brought by the advent of the next or the third generation sequencing (NGS) technologies and the dramatic drop in sequencing cost have driven biological and medical sciences to data-driven sciences. This revolutionary paradigm shift comes with challenges in terms of data transfer, storage, computation, and analysis of big bio/medical data. Cloud computing is a service model sharing a pool of configurable resources, which is a suitable workbench to address these challenges. From the medical or biological perspective, providing computing power and storage is the most attractive feature of cloud computing in handling the ever increasing biological data. As data increases in size, many research organizations start to experience the lack of computing power, which becomes a major hurdle in achieving research goals. In this paper, we review the features of publically available bio and health cloud systems in terms of graphical user interface, external data integration, security and extensibility of features. We then discuss about issues and limitations of current cloud systems and conclude with suggestion of a biological cloud environment concept, which can be defined as a total workbench environment assembling computational tools and databases for analyzing bio/medical big data in particular application domains.

Resurgence of Integrated Behavioral Units

PubMed Central

Bachá-Méndez, Gustavo; Reid, Alliston K; Mendoza-Soylovna, Adela

2007-01-01

Two experiments with rats examined the dynamics of well-learned response sequences when reinforcement contingencies were changed. Both experiments contained four phases, each of which reinforced a 2-response sequence of lever presses until responding was stable. The contingencies then were shifted to a new reinforced sequence until responding was again stable. Extinction-induced resurgence of previously reinforced, and then extinguished, heterogeneous response sequences was observed in all subjects in both experiments. These sequences were demonstrated to be integrated behavioral units, controlled by processes acting at the level of the entire sequence. Response-level processes were also simultaneously operative. Errors in sequence production were strongly influenced by the terminal, not the initial, response in the currently reinforced sequence, but not by the previously reinforced sequence. These studies demonstrate that sequence-level and response-level processes can operate simultaneously in integrated behavioral units. Resurgence and the development of integrated behavioral units may be dissociated; thus the observation of one does not necessarily imply the other. PMID:17345948

Development of a State Machine Sequencer for the Keck Interferometer: Evolution, Development and Lessons Learned using a CASE Tool Approach

NASA Technical Reports Server (NTRS)

Rede, Leonard J.; Booth, Andrew; Hsieh, Jonathon; Summer, Kellee

2004-01-01

This paper presents a discussion of the evolution of a sequencer from a simple EPICS (Experimental Physics and Industrial Control System) based sequencer into a complex implementation designed utilizing UML (Unified Modeling Language) methodologies and a CASE (Computer Aided Software Engineering) tool approach. The main purpose of the sequencer (called the IF Sequencer) is to provide overall control of the Keck Interferometer to enable science operations be carried out by a single operator (and/or observer). The interferometer links the two 10m telescopes of the W. M. Keck Observatory at Mauna Kea, Hawaii. The IF Sequencer is a high-level, multi-threaded, Hare1 finite state machine, software program designed to orchestrate several lower-level hardware and software hard real time subsystems that must perform their work in a specific and sequential order. The sequencing need not be done in hard real-time. Each state machine thread commands either a high-speed real-time multiple mode embedded controller via CORB A, or slower controllers via EPICS Channel Access interfaces. The overall operation of the system is simplified by the automation. The UML is discussed and our use of it to implement the sequencer is presented. The decision to use the Rhapsody product as our CASE tool is explained and reflected upon. Most importantly, a section on lessons learned is presented and the difficulty of integrating CASE tool automatically generated C++ code into a large control system consisting of multiple infrastructures is presented.

Development of a state machine sequencer for the Keck Interferometer: evolution, development, and lessons learned using a CASE tool approach

NASA Astrophysics Data System (ADS)

Reder, Leonard J.; Booth, Andrew; Hsieh, Jonathan; Summers, Kellee R.

2004-09-01

This paper presents a discussion of the evolution of a sequencer from a simple Experimental Physics and Industrial Control System (EPICS) based sequencer into a complex implementation designed utilizing UML (Unified Modeling Language) methodologies and a Computer Aided Software Engineering (CASE) tool approach. The main purpose of the Interferometer Sequencer (called the IF Sequencer) is to provide overall control of the Keck Interferometer to enable science operations to be carried out by a single operator (and/or observer). The interferometer links the two 10m telescopes of the W. M. Keck Observatory at Mauna Kea, Hawaii. The IF Sequencer is a high-level, multi-threaded, Harel finite state machine software program designed to orchestrate several lower-level hardware and software hard real-time subsystems that must perform their work in a specific and sequential order. The sequencing need not be done in hard real-time. Each state machine thread commands either a high-speed real-time multiple mode embedded controller via CORBA, or slower controllers via EPICS Channel Access interfaces. The overall operation of the system is simplified by the automation. The UML is discussed and our use of it to implement the sequencer is presented. The decision to use the Rhapsody product as our CASE tool is explained and reflected upon. Most importantly, a section on lessons learned is presented and the difficulty of integrating CASE tool automatically generated C++ code into a large control system consisting of multiple infrastructures is presented.

Database Resources of the BIG Data Center in 2018.

PubMed

2018-01-04

The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

PGen: large-scale genomic variations analysis workflow and browser in SoyKB.

PubMed

Liu, Yang; Khan, Saad M; Wang, Juexin; Rynge, Mats; Zhang, Yuanxun; Zeng, Shuai; Chen, Shiyuan; Maldonado Dos Santos, Joao V; Valliyodan, Babu; Calyam, Prasad P; Merchant, Nirav; Nguyen, Henry T; Xu, Dong; Joshi, Trupti

2016-10-06

With the advances in next-generation sequencing (NGS) technology and significant reductions in sequencing costs, it is now possible to sequence large collections of germplasm in crops for detecting genome-scale genetic variations and to apply the knowledge towards improvements in traits. To efficiently facilitate large-scale NGS resequencing data analysis of genomic variations, we have developed "PGen", an integrated and optimized workflow using the Extreme Science and Engineering Discovery Environment (XSEDE) high-performance computing (HPC) virtual system, iPlant cloud data storage resources and Pegasus workflow management system (Pegasus-WMS). The workflow allows users to identify single nucleotide polymorphisms (SNPs) and insertion-deletions (indels), perform SNP annotations and conduct copy number variation analyses on multiple resequencing datasets in a user-friendly and seamless way. We have developed both a Linux version in GitHub ( https://github.com/pegasus-isi/PGen-GenomicVariations-Workflow ) and a web-based implementation of the PGen workflow integrated within the Soybean Knowledge Base (SoyKB), ( http://soykb.org/Pegasus/index.php ). Using PGen, we identified 10,218,140 single-nucleotide polymorphisms (SNPs) and 1,398,982 indels from analysis of 106 soybean lines sequenced at 15X coverage. 297,245 non-synonymous SNPs and 3330 copy number variation (CNV) regions were identified from this analysis. SNPs identified using PGen from additional soybean resequencing projects adding to 500+ soybean germplasm lines in total have been integrated. These SNPs are being utilized for trait improvement using genotype to phenotype prediction approaches developed in-house. In order to browse and access NGS data easily, we have also developed an NGS resequencing data browser ( http://soykb.org/NGS_Resequence/NGS_index.php ) within SoyKB to provide easy access to SNP and downstream analysis results for soybean researchers. PGen workflow has been optimized for the most efficient analysis of soybean data using thorough testing and validation. This research serves as an example of best practices for development of genomics data analysis workflows by integrating remote HPC resources and efficient data management with ease of use for biological users. PGen workflow can also be easily customized for analysis of data in other species.

Integrating art into science education: a survey of science teachers' practices

NASA Astrophysics Data System (ADS)

Turkka, Jaakko; Haatainen, Outi; Aksela, Maija

2017-07-01

Numerous case studies suggest that integrating art and science education could engage students with creative projects and encourage students to express science in multitude of ways. However, little is known about art integration practices in everyday science teaching. With a qualitative e-survey, this study explores the art integration of science teachers (n = 66). A pedagogical model for science teachers' art integration emerged from a qualitative content analysis conducted on examples of art integration. In the model, art integration is characterised as integration through content and activities. Whilst the links in the content were facilitated either directly between concepts and ideas or indirectly through themes or artefacts, the integration through activity often connected an activity in one domain and a concept, idea or artefact in the other domain with the exception of some activities that could belong to both domains. Moreover, the examples of art integration in everyday classroom did not include expression of emotions often associated with art. In addition, quantitative part of the survey confirmed that integration is infrequent in all mapped areas. The findings of this study have implications for science teacher education that should offer opportunities for more consistent art integration.

Integrating Art into Science Education: A Survey of Science Teachers' Practices

ERIC Educational Resources Information Center

Turkka, Jaakko; Haatainen, Outi; Aksela, Maija

2017-01-01

Numerous case studies suggest that integrating art and science education could engage students with creative projects and encourage students to express science in multitude of ways. However, little is known about art integration practices in everyday science teaching. With a qualitative e-survey, this study explores the art integration of science…

Report from the NSF/SSMA Wingspread Conference: A Network for Integrated Science and Mathematics Teaching and Learning.

ERIC Educational Resources Information Center

Berlin, Donna F.; White, Arthur L.

1992-01-01

Reports the proceedings of the Wingspread conference on integrating science and mathematics teaching and learning. Discusses (1) a literature review on integration of science and mathematics education; (2) development of definitions of integration; (3) specification of guidelines for infusing integrated teaching and learning into science and…

In silico study of breast cancer associated gene 3 using LION Target Engine and other tools.

PubMed

León, Darryl A; Cànaves, Jaume M

2003-12-01

Sequence analysis of individual targets is an important step in annotation and validation. As a test case, we investigated human breast cancer associated gene 3 (BCA3) with LION Target Engine and with other bioinformatics tools. LION Target Engine confirmed that the BCA3 gene is located on 11p15.4 and that the two most likely splice variants (lacking exon 3 and exons 3 and 5, respectively) exist. Based on our manual curation of sequence data, it is proposed that an additional variant (missing only exon 5) published in a public sequence repository, is a prediction artifact. A significant number of new orthologs were also identified, and these were the basis for a high-quality protein secondary structure prediction. Moreover, our research confirmed several distinct functional domains as described in earlier reports. Sequence conservation from multiple sequence alignments, splice variant identification, secondary structure predictions, and predicted phosphorylation sites suggest that the removal of interaction sites through alternative splicing might play a modulatory role in BCA3. This in silico approach shows the depth and relevance of an analysis that can be accomplished by including a variety of publicly available tools with an integrated and customizable life science informatics platform.

How In-Service Science Teachers Integrate History and Nature of Science in Elementary Science Courses

ERIC Educational Resources Information Center

Hacieminoglu, Esme

2014-01-01

The purpose of this study is to investigate how the in-service science teachers' (IST) perceptions and practices about curriculum and integration of the history of science (HOS) and the nature of science (NOS) affect their science courses. For this aim, how ISTs integrated the NOS and HOS in their elementary science courses for understanding of…

Environmental science. Rethinking the marine carbon cycle: factoring in the multifarious lifestyles of microbes.

PubMed

Worden, Alexandra Z; Follows, Michael J; Giovannoni, Stephen J; Wilken, Susanne; Zimmerman, Amy E; Keeling, Patrick J

2015-02-13

The profound influence of marine plankton on the global carbon cycle has been recognized for decades, particularly for photosynthetic microbes that form the base of ocean food chains. However, a comprehensive model of the carbon cycle is challenged by unicellular eukaryotes (protists) having evolved complex behavioral strategies and organismal interactions that extend far beyond photosynthetic lifestyles. As is also true for multicellular eukaryotes, these strategies and their associated physiological changes are difficult to deduce from genome sequences or gene repertoires—a problem compounded by numerous unknown function proteins. Here, we explore protistan trophic modes in marine food webs and broader biogeochemical influences. We also evaluate approaches that could resolve their activities, link them to biotic and abiotic factors, and integrate them into an ecosystems biology framework. Copyright © 2015, American Association for the Advancement of Science.

Precision Medicine: From Science To Value.

PubMed

Ginsburg, Geoffrey S; Phillips, Kathryn A

2018-05-01

Precision medicine is making an impact on patients, health care delivery systems, and research participants in ways that were only imagined fifteen years ago when the human genome was first sequenced. Discovery of disease-causing and drug-response genetic variants has accelerated, while adoption into clinical medicine has lagged. We define precision medicine and the stakeholder community required to enable its integration into research and health care. We explore the intersection of data science, analytics, and precision medicine in the formation of health systems that carry out research in the context of clinical care and that optimize the tools and information used to deliver improved patient outcomes. We provide examples of real-world impact and conclude with a policy and economic agenda necessary for the adoption of this new paradigm of health care both in the United States and globally.

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

Horizontal integration of the basic sciences in the chiropractic curriculum.

PubMed

Ward, Kevin P

2010-01-01

Basic science curricula at most chiropractic colleges consist of courses (eg, general anatomy, physiology, biochemistry, etc) that are taught as stand-alone content domains. The lack of integration between basic science disciplines causes difficulties for students who need to understand how the parts function together as an integrated whole and apply this understanding to solving clinical problems. More horizontally integrated basic science curricula could be achieved by several means: integrated Part I National Board of Chiropractic Examiners questions, a broader education for future professors, an increased emphasis on integration within the current model, linked courses, and an integrated, thematic basic science curriculum. Horizontally integrating basic science curricula would require significant efforts from administrators, curriculum committees, and instructional faculty. Once in place this curriculum would promote more clinically relevant learning, improved learning outcomes, and superior vertical integration.

Horizontal Integration of the Basic Sciences in the Chiropractic Curriculum

PubMed Central

Ward, Kevin P.

2010-01-01

Basic science curricula at most chiropractic colleges consist of courses (eg, general anatomy, physiology, biochemistry, etc) that are taught as stand-alone content domains. The lack of integration between basic science disciplines causes difficulties for students who need to understand how the parts function together as an integrated whole and apply this understanding to solving clinical problems. More horizontally integrated basic science curricula could be achieved by several means: integrated Part I National Board of Chiropractic Examiners questions, a broader education for future professors, an increased emphasis on integration within the current model, linked courses, and an integrated, thematic basic science curriculum. Horizontally integrating basic science curricula would require significant efforts from administrators, curriculum committees, and instructional faculty. Once in place this curriculum would promote more clinically relevant learning, improved learning outcomes, and superior vertical integration. PMID:21048882

RoBuST: an integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae

PubMed Central

2010-01-01

Background Root and bulb vegetables (RBV) include carrots, celeriac (root celery), parsnips (Apiaceae), onions, garlic, and leek (Alliaceae)—food crops grown globally and consumed worldwide. Few data analysis platforms are currently available where data collection, annotation and integration initiatives are focused on RBV plant groups. Scientists working on RBV include breeders, geneticists, taxonomists, plant pathologists, and plant physiologists who use genomic data for a wide range of activities including the development of molecular genetic maps, delineation of taxonomic relationships, and investigation of molecular aspects of gene expression in biochemical pathways and disease responses. With genomic data coming from such diverse areas of plant science, availability of a community resource focused on these RBV data types would be of great interest to this scientific community. Description The RoBuST database has been developed to initiate a platform for collecting and organizing genomic information useful for RBV researchers. The current release of RoBuST contains genomics data for 294 Alliaceae and 816 Apiaceae plant species and has the following features: (1) comprehensive sequence annotations of 3663 genes 5959 RNAs, 22,723 ESTs and 11,438 regulatory sequence elements from Apiaceae and Alliaceae plant families; (2) graphical tools for visualization and analysis of sequence data; (3) access to traits, biosynthetic pathways, genetic linkage maps and molecular taxonomy data associated with Alliaceae and Apiaceae plants; and (4) comprehensive plant splice signal repository of 659,369 splice signals collected from 6015 plant species for comparative analysis of plant splicing patterns. Conclusions RoBuST, available at http://robust.genome.com, provides an integrated platform for researchers to effortlessly explore and analyze genomic data associated with root and bulb vegetables. PMID:20691054

Three-Year High School Science Core Curriculum: A Framework.

ERIC Educational Resources Information Center

Bardeen, Marjorie; Freeman, Wade; Lederman, Leon; Marshall, Stephanie; Thompson, Bruce; Young, M. Jean

It is time to start a complete re-structuring of the high school science sequence: new content, new instructional materials, new laboratories, new assessment tools, and new teacher preparation. This white paper initiates re-structuring by proposing organization, pedagogy, and content for a new sequence of science courses. The proposal respects the…

Exploring cognitive integration of basic science and its effect on diagnostic reasoning in novices.

PubMed

Lisk, Kristina; Agur, Anne M R; Woods, Nicole N

2016-06-01

Integration of basic and clinical science knowledge is increasingly being recognized as important for practice in the health professions. The concept of 'cognitive integration' places emphasis on the value of basic science in providing critical connections to clinical signs and symptoms while accounting for the fact that clinicians may not spontaneously articulate their use of basic science knowledge in clinical reasoning. In this study we used a diagnostic justification test to explore the impact of integrated basic science instruction on novices' diagnostic reasoning process. Participants were allocated to an integrated basic science or clinical science training group. The integrated basic science group was taught the clinical features along with the underlying causal mechanisms of four musculoskeletal pathologies while the clinical science group was taught only the clinical features. Participants completed a diagnostic accuracy test immediately after initial learning, and one week later a diagnostic accuracy and justification test. The results showed that novices who learned the integrated causal mechanisms had superior diagnostic accuracy and better understanding of the relative importance of key clinical features. These findings further our understanding of cognitive integration by providing evidence of the specific changes in clinical reasoning when basic and clinical sciences are integrated during learning.

78 FR 38318 - Integrated Science Assessment for Lead

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-26

... ENVIRONMENTAL PROTECTION AGENCY [FRL-9827-4] Integrated Science Assessment for Lead AGENCY... availability of a final document titled, ``Integrated Science Assessment for Lead'' (EPA/600/R-10/075F). The... ``Integrated Science Assessment for Lead'' will be made available primarily through the Internet on the NCEA...

More Than Words: The Role of Multiword Sequences in Language Learning and Use.

PubMed

Christiansen, Morten H; Arnon, Inbal

2017-07-01

The ability to convey our thoughts using an infinite number of linguistic expressions is one of the hallmarks of human language. Understanding the nature of the psychological mechanisms and representations that give rise to this unique productivity is a fundamental goal for the cognitive sciences. A long-standing hypothesis is that single words and rules form the basic building blocks of linguistic productivity, with multiword sequences being treated as units only in peripheral cases such as idioms. The new millennium, however, has seen a shift toward construing multiword linguistic units not as linguistic rarities, but as important building blocks for language acquisition and processing. This shift-which originated within theoretical approaches that emphasize language learning and use-has far-reaching implications for theories of language representation, processing, and acquisition. Incorporating multiword units as integral building blocks blurs the distinction between grammar and lexicon; calls for models of production and comprehension that can accommodate and give rise to the effect of multiword information on processing; and highlights the importance of such units to learning. In this special topic, we bring together cutting-edge work on multiword sequences in theoretical linguistics, first-language acquisition, psycholinguistics, computational modeling, and second-language learning to present a comprehensive overview of the prominence and importance of such units in language, their possible role in explaining differences between first- and second-language learning, and the challenges the combined findings pose for theories of language. Copyright © 2017 Cognitive Science Society, Inc.

What is bioinformatics? A proposed definition and overview of the field.

PubMed

Luscombe, N M; Greenbaum, D; Gerstein, M

2001-01-01

The recent flood of data from genome sequences and functional genomics has given rise to new field, bioinformatics, which combines elements of biology and computer science. Here we propose a definition for this new field and review some of the research that is being pursued, particularly in relation to transcriptional regulatory systems. Our definition is as follows: Bioinformatics is conceptualizing biology in terms of macromolecules (in the sense of physical-chemistry) and then applying "informatics" techniques (derived from disciplines such as applied maths, computer science, and statistics) to understand and organize the information associated with these molecules, on a large-scale. Analyses in bioinformatics predominantly focus on three types of large datasets available in molecular biology: macromolecular structures, genome sequences, and the results of functional genomics experiments (e.g. expression data). Additional information includes the text of scientific papers and "relationship data" from metabolic pathways, taxonomy trees, and protein-protein interaction networks. Bioinformatics employs a wide range of computational techniques including sequence and structural alignment, database design and data mining, macromolecular geometry, phylogenetic tree construction, prediction of protein structure and function, gene finding, and expression data clustering. The emphasis is on approaches integrating a variety of computational methods and heterogeneous data sources. Finally, bioinformatics is a practical discipline. We survey some representative applications, such as finding homologues, designing drugs, and performing large-scale censuses. Additional information pertinent to the review is available over the web at http://bioinfo.mbb.yale.edu/what-is-it.

SMITH: a LIMS for handling next-generation sequencing workflows

PubMed Central

2014-01-01

Background Life-science laboratories make increasing use of Next Generation Sequencing (NGS) for studying bio-macromolecules and their interactions. Array-based methods for measuring gene expression or protein-DNA interactions are being replaced by RNA-Seq and ChIP-Seq. Sequencing is generally performed by specialized facilities that have to keep track of sequencing requests, trace samples, ensure quality and make data available according to predefined privileges. An integrated tool helps to troubleshoot problems, to maintain a high quality standard, to reduce time and costs. Commercial and non-commercial tools called LIMS (Laboratory Information Management Systems) are available for this purpose. However, they often come at prohibitive cost and/or lack the flexibility and scalability needed to adjust seamlessly to the frequently changing protocols employed. In order to manage the flow of sequencing data produced at the Genomic Unit of the Italian Institute of Technology (IIT), we developed SMITH (Sequencing Machine Information Tracking and Handling). Methods SMITH is a web application with a MySQL server at the backend. Wet-lab scientists of the Centre for Genomic Science and database experts from the Politecnico of Milan in the context of a Genomic Data Model Project developed SMITH. The data base schema stores all the information of an NGS experiment, including the descriptions of all protocols and algorithms used in the process. Notably, an attribute-value table allows associating an unconstrained textual description to each sample and all the data produced afterwards. This method permits the creation of metadata that can be used to search the database for specific files as well as for statistical analyses. Results SMITH runs automatically and limits direct human interaction mainly to administrative tasks. SMITH data-delivery procedures were standardized making it easier for biologists and analysts to navigate the data. Automation also helps saving time. The workflows are available through an API provided by the workflow management system. The parameters and input data are passed to the workflow engine that performs de-multiplexing, quality control, alignments, etc. Conclusions SMITH standardizes, automates, and speeds up sequencing workflows. Annotation of data with key-value pairs facilitates meta-analysis. PMID:25471934

SMITH: a LIMS for handling next-generation sequencing workflows.

PubMed

Venco, Francesco; Vaskin, Yuriy; Ceol, Arnaud; Muller, Heiko

2014-01-01

Life-science laboratories make increasing use of Next Generation Sequencing (NGS) for studying bio-macromolecules and their interactions. Array-based methods for measuring gene expression or protein-DNA interactions are being replaced by RNA-Seq and ChIP-Seq. Sequencing is generally performed by specialized facilities that have to keep track of sequencing requests, trace samples, ensure quality and make data available according to predefined privileges. An integrated tool helps to troubleshoot problems, to maintain a high quality standard, to reduce time and costs. Commercial and non-commercial tools called LIMS (Laboratory Information Management Systems) are available for this purpose. However, they often come at prohibitive cost and/or lack the flexibility and scalability needed to adjust seamlessly to the frequently changing protocols employed. In order to manage the flow of sequencing data produced at the Genomic Unit of the Italian Institute of Technology (IIT), we developed SMITH (Sequencing Machine Information Tracking and Handling). SMITH is a web application with a MySQL server at the backend. Wet-lab scientists of the Centre for Genomic Science and database experts from the Politecnico of Milan in the context of a Genomic Data Model Project developed SMITH. The data base schema stores all the information of an NGS experiment, including the descriptions of all protocols and algorithms used in the process. Notably, an attribute-value table allows associating an unconstrained textual description to each sample and all the data produced afterwards. This method permits the creation of metadata that can be used to search the database for specific files as well as for statistical analyses. SMITH runs automatically and limits direct human interaction mainly to administrative tasks. SMITH data-delivery procedures were standardized making it easier for biologists and analysts to navigate the data. Automation also helps saving time. The workflows are available through an API provided by the workflow management system. The parameters and input data are passed to the workflow engine that performs de-multiplexing, quality control, alignments, etc. SMITH standardizes, automates, and speeds up sequencing workflows. Annotation of data with key-value pairs facilitates meta-analysis.

Promoting Students' Interest and Motivation Towards Science Learning: the Role of Personal Needs and Motivation Orientations

NASA Astrophysics Data System (ADS)

Loukomies, Anni; Pnevmatikos, Dimitris; Lavonen, Jari; Spyrtou, Anna; Byman, Reijo; Kariotoglou, Petros; Juuti, Kalle

2013-12-01

This study aimed to design a teaching sequence for science education that enabled lower secondary school students to enhance their motivation towards science. Further, it looked to examine the way the designed teaching sequence affected students with different motivational profiles. Industry site visits, with embodied theory-based motivational features were included as part of the designed teaching sequence. The sequence was implemented in Finland and Greece with 54 participants, 27 from each country. Quantitative data was collected using the Evaluation of Science Inquiry Activities Questionnaire, based on the Intrinsic Motivation Inventory but did not map the expected outcomes. Interviews, however, showed that students with different motivational profiles found aspects within the module that met their psychological needs as explained by Self-Determination Theory. The results offer a perspective to adolescents' psychological needs along with some insights into how students mediate the way they value an activity in the context of science education.

Opinion: Why we need a centralized repository for isotopic data

USGS Publications Warehouse

Pauli, Jonathan N.; Newsome, Seth D.; Cook, Joseph A.; Harrod, Chris; Steffan, Shawn A.; Baker, Christopher J. O.; Ben-David, Merav; Bloom, David; Bowen, Gabriel J.; Cerling, Thure E.; Cicero, Carla; Cook, Craig; Dohm, Michelle; Dharampal, Prarthana S.; Graves, Gary; Gropp, Robert; Hobson, Keith A.; Jordan, Chris; MacFadden, Bruce; Pilaar Birch, Suzanne; Poelen, Jorrit; Ratnasingham, Sujeevan; Russell, Laura; Stricker, Craig A.; Uhen, Mark D.; Yarnes, Christopher T.; Hayden, Brian

2017-01-01

Stable isotopes encode and integrate the origin of matter; thus, their analysis offers tremendous potential to address questions across diverse scientific disciplines (1, 2). Indeed, the broad applicability of stable isotopes, coupled with advancements in high-throughput analysis, have created a scientific field that is growing exponentially, and generating data at a rate paralleling the explosive rise of DNA sequencing and genomics (3). Centralized data repositories, such as GenBank, have become increasingly important as a means for archiving information, and “Big Data” analytics of these resources are revolutionizing science and everyday life.

Net current measurements and secondary electron emission characteristics of the Voyager plasma science experiment and their impact on data interpretation

NASA Technical Reports Server (NTRS)

Mcnutt, Ralph L., Jr.

1988-01-01

The Voyager Plasma Science (PLS) instrument is capable of returning integral (DC) current measurements, similar in some respects to measurements made with a Langmuir probe or a retarding potential analyzer, although there are significant differences. The integral measurements were made during a calibration sequence in the solar wind, during Cruise Science Maneuvers, and within the magnetospheres of Jupiter and Saturn by Voyager 1. After the failure of the PLS experiment following the Saturn encounter, that instrument was placed in the DC return mode returning possibly usable data from early 1981 through early 1985. The DC return measurements are difficult to interpret and are above threshold values only for relatively large fluxes; the determination of the measured current level is dependent on the operating temperature of the preamplifiers which further complicates the interpretation. Nevertheless, these measurements can be used to determine the efficiency of the suppressor grid at preventing the loss of secondary electrons off the collector plate. Some DC return measurements have been invaluable in aiding in the interpretation of some electron plasma measurements not previously understood. It is found that electron spectra can be significantly modified by the presence of second generation secondary electrons produced by either first generation secondaries or photoelectrons on the support ring of the negative high voltage modulator grid within the instrument housing.

Doctoral conceptual thresholds in cellular and molecular biology

NASA Astrophysics Data System (ADS)

Feldon, David F.; Rates, Christopher; Sun, Chongning

2017-12-01

In the biological sciences, very little is known about the mechanisms by which doctoral students acquire the skills they need to become independent scientists. In the postsecondary biology education literature, identification of specific skills and effective methods for helping students to acquire them are limited to undergraduate education. To establish a foundation from which to investigate the developmental trajectory of biologists' research skills, it is necessary to identify those skills which are integral to doctoral study and distinct from skills acquired earlier in students' educational pathways. In this context, the current study engages the framework of threshold concepts to identify candidate skills that are both obstacles and significant opportunities for developing proficiency in conducting research. Such threshold concepts are typically characterised as transformative, integrative, irreversible, and challenging. The results from interviews and focus groups with current and former doctoral students in cellular and molecular biology suggest two such threshold concepts relevant to their subfield: the first is an ability to effectively engage primary research literature from the biological sciences in a way that is critical without dismissing the value of its contributions. The second is the ability to conceptualise appropriate control conditions necessary to design and interpret the results of experiments in an efficient and effective manner for research in the biological sciences as a discipline. Implications for prioritising and sequencing graduate training experiences are discussed on the basis of the identified thresholds.

(abstract) Science-Project Interaction in the Low-Cost Mission

NASA Technical Reports Server (NTRS)

Wall, Stephen D.

1994-01-01

Large, complex, and highly optimized missions have performed most of the preliminary reconnaisance of the solar system. As a result we have now mapped significant fractions of its total surface (or surface-equivalent) area. Now, however, scientific exploration of the solar system is undergoing a major change in scale, and existing missions find it necessary to limit costs while fulfilling existing goals. In the future, NASA's Discovery program will continue the reconnaisance, exploration, and diagnostic phases of planetary research using lower cost missions, which will include lower cost mission operations systems (MOS). Historically, one of the more expensive functions of MOS has been its interaction with the science community. Traditional MOS elements that this interaction have embraced include mission planning, science (and engineering) event conflict resolution, sequence optimization and integration, data production (e.g., assembly, enhancement, quality assurance, documentation, archive), and other science support services. In the past, the payoff from these efforts has been that use of mission resources has been highly optimized, constraining resources have been generally completely consumed, and data products have been accurate and well documented. But because these functions are expensive we are now challenged to reduce their cost while preserving the benefits. In this paper, we will consider ways of revising the traditional MOS approach that might save project resources while retaining a high degree of service to the Projects' customers. Pre-launch, science interaction can be made simplier by limiting numbers of instruments and by providing greater redundancy in mission plans. Post launch, possibilities include prioritizing data collection into a few categories, easing requirements on real-time of quick-look data delivery, and closer integration of scientists into the mission operation.

A New Era of Science Education: Science Teachers' Perceptions and Classroom Practices of Science, Technology, Engineering, and Mathematics (STEM) Integration

NASA Astrophysics Data System (ADS)

Wang, Hui-Hui

Quality STEM education is the key in helping the United States maintain its lead in global competitiveness and in preparing for new economic and security challenges in the future. Policymakers and professional societies emphasize STEM education by legislating the addition of engineering standards to the existing science standards. On the other hand, the nature of the work of most STEM professionals requires people to actively apply STEM knowledge to make critical decisions. Therefore, using an integrated approach to teaching STEM in K-12 is expected. However, science teachers encounter numerous difficulties in adapting the new STEM integration reforms into their classrooms because of a lack of knowledge and experience. Therefore, high quality STEM integration professional development programs are an urgent necessity. In order to provide these high quality programs, it is important to understand teachers' perceptions and classroom practices regarding STEM integration. A multiple-case study was conducted with five secondary school science teachers in order to gain a better understanding of teachers' perceptions and classroom practices in using STEM integration. This study addresses the following research questions: 1) What are secondary school science teachers' practices of STEM integration? 2) What are secondary science teachers' overall perceptions of STEM integration? and 3) What is the connection between secondary science teachers' perceptions and understanding of STEM integration with their classroom practices? This research aims to explore teachers' perceptions and classroom practices in order to set up the baseline for STEM integration and also to determine STEM integration professional development best practices in science education. Findings from the study provide critical data for making informed decision about the direction for STEM integration in science education in K-12.

Climate Science Program at California State University, Northridge

NASA Astrophysics Data System (ADS)

Steele Cox, H.; Klein, D.; Cadavid, A. C.; Foley, B.

2012-12-01

Due to its interdisciplinary nature, climate science poses wide-ranging challenges for science and mathematics students seeking careers in this field. There is a compelling need for universities to provide coherent programs in climate science in order to train future climate scientists. With funding from NASA Innovations in Climate Education (NICE), California State University, Northridge (CSUN), is creating the CSUN Climate Science Program. An interdisciplinary team of faculty members is working in collaboration with UCLA, Santa Monica College and NASA/JPL partners to create a new curriculum in climate science. The resulting sequence of climate science courses, or Pathway for studying the Mathematics of Climate Change (PMCC), is integrated into a Bachelor of Science degree program in the Applied Mathematical Sciences offered by the Mathematics Department at CSUN. The PMCC consists of courses offered by the departments of Mathematics, Physics, and Geography and is designed to prepare students for Ph.D. programs in technical fields relevant to global climate change and related careers. The students who choose to follow this program will be guided to enroll in the following sequence of courses for their 12 units of upper division electives: 1) A newly created course junior level course, Math 396CL, in applied mathematics which will introduce students to applications of vector calculus and differential equations to the study of thermodynamics and atmospheric dynamics. 2) An already existing course, Math 483, with new content on mathematical modeling specialized for this program; 3) An improved version of Phys 595CL on the mathematics and physics of climate change with emphasis on Radiative Transfer; 4) A choice of Geog 407 on Remote Sensing or Geog 416 on Climate Change with updated content to train the students in the analysis of satellite data obtained with the NASA Earth Observing System and instruction in the analysis of data obtained within a Geographical Information System (GIS). In addition the Geography department will similarly update the corresponding graduate courses on Remote Sensing, Geog 690D, and Climate Change Geog 620F, and there will be a reciprocal curriculum and data sharing collaboration with the Earth and Environmental Sciences program at Santa Monica College. Throughout the academic year a seminar series offers the students the opportunity to learn about ongoing work on Atmospheric Sciences and Climate and during the summer they have access to research experiences at NASA's Jet Propulsion Laboratory.

Submitting MIGS, MIMS, MIENS Information to EMBL and Standards and the Sequencing Pipelines of the Gordon and Betty Moore Foundation (GSC8 Meeting)

ScienceCinema

Vaughan, Bob; Kaye, Jon

2018-01-24

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Bob Vaughan of EMBL on submitting MIGS/MIMS/MIENS information to EMBL-EBI's system, followed by a brief talk from Jon Kaye of the Gordon and Betty Moore Foundation on standards and the foundation's sequencing pipelines at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.

Submitting MIGS, MIMS, MIENS Information to EMBL and Standards and the Sequencing Pipelines of the Gordon and Betty Moore Foundation (GSC8 Meeting)

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

Vaughan, Bob; Kaye, Jon

2009-09-09

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Bob Vaughan of EMBL on submitting MIGS/MIMS/MIENS information to EMBL-EBI's system, followed by a brief talk from Jon Kaye of the Gordon and Bettymore » Moore Foundation on standards and the foundation's sequencing pipelines at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.« less

Promoting Students' Interest and Motivation towards Science Learning: The Role of Personal Needs and Motivation Orientations

ERIC Educational Resources Information Center

Loukomies, Anni; Pnevmatikos, Dimitris; Lavonen, Jari; Spyrtou, Anna; Byman, Reijo; Kariotoglou, Petros; Juuti, Kalle

2013-01-01

This study aimed to design a teaching sequence for science education that enabled lower secondary school students to enhance their motivation towards science. Further, it looked to examine the way the designed teaching sequence affected students with different motivational profiles. Industry site visits, with embodied theory-based motivational…

Integrating Science in Agricultural Education: Attitudes of Indiana Agricultural Science and Business Teachers.

ERIC Educational Resources Information Center

Balschweid, Mark A.; Thompson, Gregory W.

2002-01-01

In a survey of Indiana agriscience and business teachers (n=170), one-half reported their students receive science credit for agriscience and business courses; they felt prepared to teach integrated biological sciences; and integration required more preparation time. They needed appropriate equipment and adequate funding to support integration.…

An Instrumental Case Study of Effective Science Integration in a Traditional Agricultural Education Program

ERIC Educational Resources Information Center

Baker, Marshall A.; Bunch, J. C.; Kelsey, Kathleen D.

2015-01-01

The integration of science and agriculture has been discussed since the inception of agricultural education. However, the standards-based focus in public secondary education and changing climate of agriculture has brought science integration back to the forefront. Though research has indicated that the integration of science into agricultural…

Examining Thai high school students' developing STEM projects

NASA Astrophysics Data System (ADS)

Teenoi, Kultida; Siripun, Kulpatsorn; Yuenyong, Chokchai

2018-01-01

Like others, Thailand education strongly focused on STEM education. This paper aimed to examine existing Thai high school students' integrated knowledge about science, technology, engineering, and mathematics (STEM) in their developing science project. The participants included 49 high school students were studying the subject of individual study (IS) in Khon Kaen wittayayon school, Khon Kaen, Thailand. The IS was provided to gradually enhance students to know how to do science project starting from getting start to do science projects, They enrolled to study the individual study of science project for three year in roll. Methodology was qualitative research. Views of students' integrated knowledge about STEM were interpreted through participant observation, interview, and students' science projects. The first author as participant observation has taught this group of students for 3 years. It found that 16 science projects were developed. Views of students' integrated knowledge about STEM could be categorized into three categories. These included (1) completely indicated integration of knowledge about science, technology, engineering, and mathematics, (2) partial indicated integration of knowledge about science, technology, engineering, and mathematics, and (3) no integration. The findings revealed that majority of science projects could be categorized as completely indicated integration of knowledge about science, technology, engineering, and mathematics. The paper suggested some ideas of enhancing students to applying STEM for developing science projects.

Barriers, Support, and Collaboration: A Comparison of Science and Agriculture Teachers' Perceptions regarding Integration of Science into the Agricultural Education Curriculum

ERIC Educational Resources Information Center

Warnick, Brian K.; Thompson, Gregory W.

2007-01-01

This study is part of a larger investigation which focused on determining and comparing the perceptions of agriculture teachers and science teachers on integrating science into agricultural education programs. Science and agriculture teachers' perceptions of barriers to integrating science, the support of stakeholders, and collaboration between…

Children's Representation and Imitation of Events: How Goal Organization Influences 3-Year-Old Children's Memory for Action Sequences.

PubMed

Loucks, Jeff; Mutschler, Christina; Meltzoff, Andrew N

2017-09-01

Children's imitation of adults plays a prominent role in human cognitive development. However, few studies have investigated how children represent the complex structure of observed actions which underlies their imitation. We integrate theories of action segmentation, memory, and imitation to investigate whether children's event representation is organized according to veridical serial order or a higher level goal structure. Children were randomly assigned to learn novel event sequences either through interactive hands-on experience (Study 1) or via storybook (Study 2). Results demonstrate that children's representation of observed actions is organized according to higher level goals, even at the cost of representing the veridical temporal ordering of the sequence. We argue that prioritizing goal structure enhances event memory, and that this mental organization is a key mechanism of social-cognitive development in real-world, dynamic environments. It supports cultural learning and imitation in ecologically valid settings when social agents are multitasking and not demonstrating one isolated goal at a time. Copyright © 2016 Cognitive Science Society, Inc.

Examining the Effects of Integrated Science, Engineering, and Nonfiction Literature on Student Learning in Elementary Classrooms

NASA Astrophysics Data System (ADS)

Tank, Kristina Maruyama

In recent years there has been an increasing emphasis on the integration of multiple disciplines in order to help prepare more students to better address the complex challenges they will face in the 21st century. Exposing students to an integrated and multidisciplinary approach will help them to better understand the connections between subjects instead of as individual and separate subjects. Science, Technology, Engineering and Mathematics (STEM) Integration has been suggested as an approach that would model a multidisciplinary approach while also offering authentic and meaningful learning experiences to students. However, there is limited research on STEM integration in the elementary classroom and additional research is needed to better define and explore the effects of this integration for both students and science educators. With the recent recommendations for teaching both science and engineering in elementary classrooms (NRC, 2012), two common models include teaching science through inquiry and teaching science through engineering-design pedagogies. This study will explore both of these models as it seeks to better understand one piece of the larger issue of STEM and STEM integration by examining how the integration of science, engineering, and nonfiction literature affects students learning in elementary classrooms. This study employed an embedded mixed methods design to measure the effects of this integration on student learning in four fifth grade classrooms from the same elementary school. The findings revealed that the students who participated in the nonfiction reading instruction that was integrated with their science instruction showed a greater increase in all measures of student learning in both science and reading when compared to the control students. The findings from the integrated science, engineering and nonfiction literature revealed similar findings with the treatment students showing a greater increase in the measures of student learning in all three of the content areas. These results suggest that integrating nonfiction literature with science or science and engineering instruction can be an effective strategy in improving student learning in elementary classrooms.

Practical Insights into Curricula Integration for Primary Science

ERIC Educational Resources Information Center

Hudson, Peter

2012-01-01

As indicated in a previous Teaching Science article, effective planning for curricula integration requires using standards from two (or more) subject areas (e.g., Science and English, Science and Art or Science and Mathematics), which also becomes the assessment foci for teaching and learning. Curricula integration of standards into an activity…

Quasi-integrability in the modified defocusing non-linear Schrödinger model and dark solitons

NASA Astrophysics Data System (ADS)

Blas, H.; Zambrano, M.

2016-03-01

The concept of quasi-integrability has been examined in the context of deformations of the defocusing non-linear Schrödinger model (NLS). Our results show that the quasi-integrability concept, recently discussed in the context of deformations of the sine-Gordon, Bullough-Dodd and focusing NLS models, holds for the modified defocusing NLS model with dark soliton solutions and it exhibits the new feature of an infinite sequence of alternating conserved and asymptotically conserved charges. For the special case of two dark soliton solutions, where the field components are eigenstates of a space-reflection symmetry, the first four and the sequence of even order charges are exactly conserved in the scattering process of the solitons. Such results are obtained through analytical and numerical methods, and employ adaptations of algebraic techniques used in integrable field theories. We perform extensive numerical simulations and consider the scattering of dark solitons for the cubic-quintic NLS model with potential V=η {I}^2-in /6{I}^3 and the saturable type potential satisfying [InlineEquation not available: see fulltext.], with a deformation parameter ɛ ∈ [InlineMediaObject not available: see fulltext.] and I = | ψ|2. The issue of the renormalization of the charges and anomalies, and their (quasi)conservation laws are properly addressed. The saturable NLS supports elastic scattering of two soliton solutions for a wide range of values of { η, ɛ, q}. Our results may find potential applications in several areas of non-linear science, such as the Bose-Einstein condensation.

Alzheimer's disease in the omics era.

PubMed

Sancesario, Giulia M; Bernardini, Sergio

2018-06-18

Recent progresses in high-throughput technologies have led to a new scenario in investigating pathologies, named the "Omics era", which integrate the opportunity to collect large amounts of data and information at the molecular and protein levels together with the development of novel computational and statistical tools that are able to analyze and filter such data. Subsequently, advances in genotyping arrays, next generation sequencing, mass spectrometry technology, and bioinformatics allowed for the simultaneous large-scale study of thousands of genes (genomics), epigenetics factors (epigenomics), RNA (transcriptomics), metabolites (metabolomics) and proteins(proteomics), with the possibility of integrating multiple types of omics data ("multi -omics"). All of these technological innovations have modified the approach to the study of complex diseases, such as Alzheimer's Disease (AD), thus representing a promising tool to investigate the relationship between several molecular pathways in AD as well as other pathologies. This review focuses on the current knowledge on the pathology of AD, the recent findings from Omics sciences, and the challenge of the use of Big Data. We then focus on future perspectives for Omics sciences, such as the discovery of novel diagnostic biomarkers or drugs. Copyright © 2018. Published by Elsevier Inc.

Genome Science: A Video Tour of the Washington University Genome Sequencing Center for High School and Undergraduate Students

PubMed Central

2005-01-01

Sequencing of the human genome has ushered in a new era of biology. The technologies developed to facilitate the sequencing of the human genome are now being applied to the sequencing of other genomes. In 2004, a partnership was formed between Washington University School of Medicine Genome Sequencing Center's Outreach Program and Washington University Department of Biology Science Outreach to create a video tour depicting the processes involved in large-scale sequencing. “Sequencing a Genome: Inside the Washington University Genome Sequencing Center” is a tour of the laboratory that follows the steps in the sequencing pipeline, interspersed with animated explanations of the scientific procedures used at the facility. Accompanying interviews with the staff illustrate different entry levels for a career in genome science. This video project serves as an example of how research and academic institutions can provide teachers and students with access and exposure to innovative technologies at the forefront of biomedical research. Initial feedback on the video from undergraduate students, high school teachers, and high school students provides suggestions for use of this video in a classroom setting to supplement present curricula. PMID:16341256

Enhancing Teacher Preparation and Improving Faculty Teaching Skills: Lessons Learned from Implementing ``Science That Matters'' a Standards Based Interdisciplinary Science Course Sequence

NASA Astrophysics Data System (ADS)

Potter, Robert; Meisels, Gerry

2005-06-01

In a highly collaborative process we developed an introductory science course sequence to improve science literacy especially among future elementary and middle school education majors. The materials and course features were designed using the results of research on teaching and learning to provide a rigorous, relevant and engaging, standard based science experience. More than ten years of combined planning, development, implementation and assessment of this college science course sequence for nonmajors/future teachers has provided significant insights and success in achieving our goal. This paper describes the history and iterative nature of our ongoing improvements, changes in faculty instructional practice, strategies used to overcome student resistance, significant student learning outcomes, support structures for faculty, and the essential and informative role of assessment in improving the outcomes. Our experience with diverse institutions, students and faculty provides the basis for the lessons we have learned and should be of help to others involved in advancing science education.

Virus-Clip: a fast and memory-efficient viral integration site detection tool at single-base resolution with annotation capability.

PubMed

Ho, Daniel W H; Sze, Karen M F; Ng, Irene O L

2015-08-28

Viral integration into the human genome upon infection is an important risk factor for various human malignancies. We developed viral integration site detection tool called Virus-Clip, which makes use of information extracted from soft-clipped sequencing reads to identify exact positions of human and virus breakpoints of integration events. With initial read alignment to virus reference genome and streamlined procedures, Virus-Clip delivers a simple, fast and memory-efficient solution to viral integration site detection. Moreover, it can also automatically annotate the integration events with the corresponding affected human genes. Virus-Clip has been verified using whole-transcriptome sequencing data and its detection was validated to have satisfactory sensitivity and specificity. Marked advancement in performance was detected, compared to existing tools. It is applicable to versatile types of data including whole-genome sequencing, whole-transcriptome sequencing, and targeted sequencing. Virus-Clip is available at http://web.hku.hk/~dwhho/Virus-Clip.zip.

PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities.

PubMed

Troshin, Peter V; Postis, Vincent Lg; Ashworth, Denise; Baldwin, Stephen A; McPherson, Michael J; Barton, Geoffrey J

2011-03-07

Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS) that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/.

MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands

PubMed Central

Ou, Hong-Yu; He, Xinyi; Harrison, Ewan M.; Kulasekara, Bridget R.; Thani, Ali Bin; Kadioglu, Aras; Lory, Stephen; Hinton, Jay C. D.; Barer, Michael R.; Rajakumar, Kumar

2007-01-01

MobilomeFINDER (http://mml.sjtu.edu.cn/MobilomeFINDER) is an interactive online tool that facilitates bacterial genomic island or ‘mobile genome’ (mobilome) discovery; it integrates the ArrayOme and tRNAcc software packages. ArrayOme utilizes a microarray-derived comparative genomic hybridization input data set to generate ‘inferred contigs’ produced by merging adjacent genes classified as ‘present’. Collectively these ‘fragments’ represent a hypothetical ‘microarray-visualized genome (MVG)’. ArrayOme permits recognition of discordances between physical genome and MVG sizes, thereby enabling identification of strains rich in microarray-elusive novel genes. Individual tRNAcc tools facilitate automated identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites and other integration hotspots in closely related sequenced genomes. Accessory tools facilitate design of hotspot-flanking primers for in silico and/or wet-science-based interrogation of cognate loci in unsequenced strains and analysis of islands for features suggestive of foreign origins; island-specific and genome-contextual features are tabulated and represented in schematic and graphical forms. To date we have used MobilomeFINDER to analyse several Enterobacteriaceae, Pseudomonas aeruginosa and Streptococcus suis genomes. MobilomeFINDER enables high-throughput island identification and characterization through increased exploitation of emerging sequence data and PCR-based profiling of unsequenced test strains; subsequent targeted yeast recombination-based capture permits full-length sequencing and detailed functional studies of novel genomic islands. PMID:17537813

The LAM-PCR Method to Sequence LV Integration Sites.

PubMed

Wang, Wei; Bartholomae, Cynthia C; Gabriel, Richard; Deichmann, Annette; Schmidt, Manfred

2016-01-01

Integrating viral gene transfer vectors are commonly used gene delivery tools in clinical gene therapy trials providing stable integration and continuous gene expression of the transgene in the treated host cell. However, integration of the reverse-transcribed vector DNA into the host genome is a potentially mutagenic event that may directly contribute to unwanted side effects. A comprehensive and accurate analysis of the integration site (IS) repertoire is indispensable to study clonality in transduced cells obtained from patients undergoing gene therapy and to identify potential in vivo selection of affected cell clones. To date, next-generation sequencing (NGS) of vector-genome junctions allows sophisticated studies on the integration repertoire in vitro and in vivo. We have explored the use of the Illumina MiSeq Personal Sequencer platform to sequence vector ISs amplified by non-restrictive linear amplification-mediated PCR (nrLAM-PCR) and LAM-PCR. MiSeq-based high-quality IS sequence retrieval is accomplished by the introduction of a double-barcode strategy that substantially minimizes the frequency of IS sequence collisions compared to the conventionally used single-barcode protocol. Here, we present an updated protocol of (nr)LAM-PCR for the analysis of lentiviral IS using a double-barcode system and followed by deep sequencing using the MiSeq device.

Physical Science Teachers' Attitudes to and Factors Affecting Their Integration of Technology Education in Science Teaching in Benin

ERIC Educational Resources Information Center

Kelani, Raphael R.; Gado, Issaou

2018-01-01

Following the calls of international conferences related to the teaching of science and technology, technology education (TE) was integrated as a component of physical sciences programmes in Benin, West Africa. This study investigates physical science teachers' attitudes towards the integration of TE topics in secondary school science curricula in…

Integrated Medical Curriculum: Advantages and Disadvantages

PubMed Central

Quintero, Gustavo A.; Vergel, John; Arredondo, Martha; Ariza, María-Cristina; Gómez, Paula; Pinzon-Barrios, Ana-Maria

2016-01-01

Most curricula for medical education have been integrated horizontally and vertically–-vertically between basic and clinical sciences. The Flexnerian curriculum has disappeared to permit integration between basic sciences and clinical sciences, which are taught throughout the curriculum. We have proposed a different form of integration where the horizontal axis represents the defined learning outcomes and the vertical axis represents the teaching of the sciences throughout the courses. We believe that a mere integration of basic and clinical sciences is not enough because it is necessary to emphasize the importance of humanism as well as health population sciences in medicine. It is necessary to integrate basic and clinical sciences, humanism, and health population in the vertical axis, not only in the early years but also throughout the curriculum, presupposing the use of active teaching methods based on problems or cases in small groups. PMID:29349303

The Importance of Agriculture Science Course Sequencing in High Schools: A View from Collegiate Agriculture Students

ERIC Educational Resources Information Center

Wheelus, Robin P.

2009-01-01

The objective of this study was to investigate the importance of Agriculture Science course sequencing in high schools, as a preparatory factor for students enrolled in collegiate agriculture classes. With the variety of courses listed in the Texas Essential Knowledge and Skills (TEKS) for Agriculture Science, it has been possible for counselors,…

Characterizing Middle Grade Students' Integrated Alternative Science Knowledge about the Effects of Climate Change

ERIC Educational Resources Information Center

Fick, Sarah J.; Songer, Nancy Butler

2017-01-01

Recent reforms emphasize a shift in how students should learn and demonstrate knowledge of science. These reforms call for students to learn content knowledge using science and engineering practices, creating integrated science knowledge. While there is existing literature about the development of integrated science knowledge assessments, few…

Integrating Mathematics and Science: Ecology and Venn Diagrams

ERIC Educational Resources Information Center

Leszczynski, Eliza; Munakata, Mika; Evans, Jessica M.; Pizzigoni, Francesca

2014-01-01

Efforts to integrate mathematics and science have been widely recognized by mathematics and science educators. However, successful integration of these two important school disciplines remains a challenge. In this article, a mathematics and science activity extends the use of Venn diagrams to a life science context and then circles back to a…

Two Related Parametric Integrals

ERIC Educational Resources Information Center

Dana-Picard, T.

2007-01-01

Two related sequences of definite integrals are considered. By mixing hand-work, computer algebra system assistance and websurfing, fine connections can be studied between integrals and a couple of interesting sequences of integers. (Contains 4 tables.)

Automatic liquid handling for life science: a critical review of the current state of the art.

PubMed

Kong, Fanwei; Yuan, Liang; Zheng, Yuan F; Chen, Weidong

2012-06-01

Liquid handling plays a pivotal role in life science laboratories. In experiments such as gene sequencing, protein crystallization, antibody testing, and drug screening, liquid biosamples frequently must be transferred between containers of varying sizes and/or dispensed onto substrates of varying types. The sample volumes are usually small, at the micro- or nanoliter level, and the number of transferred samples can be huge when investigating large-scope combinatorial conditions. Under these conditions, liquid handling by hand is tedious, time-consuming, and impractical. Consequently, there is a strong demand for automated liquid-handling methods such as sensor-integrated robotic systems. In this article, we survey the current state of the art in automatic liquid handling, including technologies developed by both industry and research institutions. We focus on methods for dealing with small volumes at high throughput and point out challenges for future advancements.

Precision Medicine: From Science to Value

PubMed Central

Ginsburg, Geoffrey S; Phillips, Kathryn A

2018-01-01

Precision medicine is poised to have an impact on patients, health care delivery systems and research participants in ways that were only imagined 15 years ago when the human genome was first sequenced. While discovery using genome-based technologies has accelerated, these have only begun to be adopted into clinical medicine. Here we define precision medicine and the stakeholder ecosystem required to enable its integration into research and health care. We explore the intersection of data science, analytics and precision medicine in creating a learning health system that carries out research in the context of clinical care and at the same time optimizes the tools and information used to delivery improved patient outcomes. We provide examples of real world impact, and conclude with a policy and economic agenda that will be necessary for the adoption of this new paradigm of health care both in the United States and globally. PMID:29733705

Building the Capacity for Climate Services: Thoughts on Training Next Generation Climate Science Integrators

NASA Astrophysics Data System (ADS)

Garfin, G. M.; Brugger, J.; Gordon, E. S.; Barsugli, J. J.; Rangwala, I.; Travis, W.

2015-12-01

For more than a decade, stakeholder needs assessments and reports, including the recent National Climate Assessment, have pointed out the need for climate "science translators" or "science integrators" who can help bridge the gap between the cultures and contexts of researchers and decision-makers. Integration is important for exchanging and enhancing knowledge, building capacity to use climate information in decision making, and fostering more robust planning for decision-making in the context of climate change. This talk will report on the characteristics of successful climate science integrators, and a variety of models for training the upcoming generation of climate science integrators. Science integration characteristics identified by an experienced vanguard in the U.S. include maintaining credibility in both the scientific and stakeholder communities, a basic respect for stakeholders demonstrated through active listening, and a deep understanding of the decision-making context. Drawing upon the lessons of training programs for Cooperative Extension, public health professionals, and natural resource managers, we offer ideas about training next generation climate science integrators. Our model combines training and development of skills in interpersonal relations, communication of science, project implementation, education techniques and practices - integrated with a strong foundation in disciplinary knowledge.

Alteration of gene expression in human hepatocellular carcinoma with integrated hepatitis B virus DNA.

PubMed

Tamori, Akihiro; Yamanishi, Yoshihiro; Kawashima, Shuichi; Kanehisa, Minoru; Enomoto, Masaru; Tanaka, Hiromu; Kubo, Shoji; Shiomi, Susumu; Nishiguchi, Shuhei

2005-08-15

Integration of hepatitis B virus (HBV) DNA into the human genome is one of the most important steps in HBV-related carcinogenesis. This study attempted to find the link between HBV DNA, the adjoining cellular sequence, and altered gene expression in hepatocellular carcinoma (HCC) with integrated HBV DNA. We examined 15 cases of HCC infected with HBV by cassette ligation-mediated PCR. The human DNA adjacent to the integrated HBV DNA was sequenced. Protein coding sequences were searched for in the human sequence. In five cases with HBV DNA integration, from which good quality RNA was extracted, gene expression was examined by cDNA microarray analysis. The human DNA sequence successive to integrated HBV DNA was determined in the 15 HCCs. Eight protein-coding regions were involved: ras-responsive element binding protein 1, calmodulin 1, mixed lineage leukemia 2 (MLL2), FLJ333655, LOC220272, LOC255345, LOC220220, and LOC168991. The MLL2 gene was expressed in three cases with HBV DNA integrated into exon 3 of MLL2 and in one case with HBV DNA integrated into intron 3 of MLL2. Gene expression analysis suggested that two HCCs with HBV integrated into MLL2 had similar patterns of gene expression compared with three HCCs with HBV integrated into other loci of human chromosomes. HBV DNA was integrated at random sites of human DNA, and the MLL2 gene was one of the targets for integration. Our results suggest that HBV DNA might modulate human genes near integration sites, followed by integration site-specific expression of such genes during hepatocarcinogenesis.

Characterization of the genetic elements required for site-specific integration of plasmid pSE211 in Saccharopolyspora erythraea.

PubMed Central

Brown, D P; Idler, K B; Katz, L

1990-01-01

The 18.1-kilobase plasmid pSE211 integrates into the chromosome of Saccharopolyspora erythraea at a specific attB site. Restriction analysis of the integrated plasmid, pSE211int, and adjacent chromosomal sequences allowed identification of attP, the plasmid attachment site. Nucleotide sequencing of attP, attB, attL, and attR revealed a 57-base-pair sequence common to all sites with no duplications of adjacent plasmid or chromosomal sequences in the integrated state, indicating that integration takes place through conservative, reciprocal strand exchange. An analysis of the sequences indicated the presence of a putative gene for Phe-tRNA at attB which is preserved at attL after integration has occurred. A comparison of the attB site for a number of actinomycete plasmids is presented. Integration at attB was also observed when a 2.4-kilobase segment of pSE211 containing attP and the adjacent plasmid sequence was used to transform a pSE211- host. Nucleotide sequencing of this segment revealed the presence of two complete open reading frames (ORFs) and a segment of a third ORF. The ORF adjacent to attP encodes a putative polypeptide 437 amino acids in length that shows similarity, at its C-terminal domain, to sequences of site-specific recombinases of the integrase family. The adjacent ORF encodes a putative 98-amino-acid basic polypeptide that contains a helix-turn-helix motif at its N terminus which corresponds to domains in the Xis proteins of a number of bacteriophages. A proposal for the function of this polypeptide is presented. The deduced amino acid sequence of the third ORF did not reveal similarities to polypeptide sequences in the current data banks. Images FIG. 2 FIG. 3 PMID:2180909

CTE Teachers' Perspectives on the Process of CTE and Science Content Integration: A Grounded Theory

NASA Astrophysics Data System (ADS)

Spindler, Matthew Kenneth

The integration of career and technical education (CTE) and academic curricular content that capitalizes on natural and inherent connections represents a challenge for CTE professionals. The research question that was used to guide the current study was: What are CTE teachers' perspectives of and experiences with the process of CTE and science content integration? And more specifically, to generate a grounded theory which explicates the process of CTE and science content integration from the perspective of CTE teachers. The CTE teachers expressed that the process of CTE and science content integration was a process of evolutionizing. From the perspective of the CTE teachers involved integrating CTE and science content resulted in their programs of study being adapted into something different than they were before the process of integration was begun. The CTE teachers revealed that the evolutions in their programs of study and themselves were associated with three other categories within the grounded theory: (a) connecting; (b) enacting; and (c) futuring. The process of CTE and science content integration represents a deep and complex episode for CTE teachers. The process of CTE and science content integration requires connecting to others, putting ideas into action, and an orienting towards the future.

Designing Better Scaffolding in Teaching Complex Systems with Graphical Simulations

NASA Astrophysics Data System (ADS)

Li, Na

Complex systems are an important topic in science education today, but they are usually difficult for secondary-level students to learn. Although graphic simulations have many advantages in teaching complex systems, scaffolding is a critical factor for effective learning. This dissertation study was conducted around two complementary research questions on scaffolding: (1) How can we chunk and sequence learning activities in teaching complex systems? (2) How can we help students make connections among system levels across learning activities (level bridging)? With a sample of 123 seventh-graders, this study employed a 3x2 experimental design that factored sequencing methods (independent variable 1; three levels) with level-bridging scaffolding (independent variable 2; two levels) and compared the effectiveness of each combination. The study measured two dependent variables: (1) knowledge integration (i.e., integrating and connecting content-specific normative concepts and providing coherent scientific explanations); (2) understanding of the deep causal structure (i.e., being able to grasp and transfer the causal knowledge of a complex system). The study used a computer-based simulation environment as the research platform to teach the ideal gas law as a system. The ideal gas law is an emergent chemical system that has three levels: (1) experiential macro level (EM) (e.g., an aerosol can explodes when it is thrown into the fire); (2) abstract macro level (AM) (i.e., the relationships among temperature, pressure and volume); (3) micro level (Mi) (i.e., molecular activity). The sequencing methods of these levels were manipulated by changing the order in which they were delivered with three possibilities: (1) EM-AM-Mi; (2) Mi-AM-EM; (3) AM-Mi-EM. The level-bridging scaffolding variable was manipulated on two aspects: (1) inserting inter-level questions among learning activities; (2) two simulations dynamically linked in the final learning activity. Addressing the first research question, the Experiential macro-Abstract macro-Micro (EM-AM-Mi) sequencing method, following the "concrete to abstract" principle, produced better knowledge integration while the Micro-Abstract macro-Experiential macro (Mi-AM-EM) sequencing method, congruent with the causal direction of the emergent system, produced better understanding of the deep causal structure only when level-bridging scaffolding was provided. The Abstract macro-Micro-Experiential macro (AM-Mi-EM) sequencing method produced worse performance in general, because it did not follow the "concrete to abstract" principle, nor did it align with the causal structure of the emergent system. As to the second research question, the results showed that level-bridging scaffolding was important for both knowledge integration and understanding of the causal structure in learning the ideal gas law system.

Zymomonas pentose-sugar fermenting strains and uses thereof

DOEpatents

Zhang, Min [Lakewood, CO; Chou, Yat-Chen [Golden, CO; Howe, William [Golden, CO; Eddy, Christine [Golden, CO; Evans, Kent [Littleton, CO; Mohagheghi, Ali [Northglenn, CO

2007-05-29

Disclosed in the present invention is a Zymomonas integrant and derivatives of these integrants that posses the ability to ferment pentose into ethanol. The genetic sequences encoding for the pentose-fermenting enzymes are integrated into the Zymomonas in a two-integration event of homologous recombination and transposition. Each operon includes more than one pentose-reducing enzyme encoding sequence. The integrant in some embodiments includes enzyme sequences encoding xylose isomerase, xylulokinase, transketolase and transketolase. The Zymomonas integrants are highly stable, and retain activity for producing the pentose-fermenting enzyme for between 80 to 160 generations. The integrants are also resistant to acetate inhibition, as the integrants demonstrate efficient ethanol production even in the presence of 8 up to 16 grams acetate per liter media. These stably integrated sequences provide a unique Zymomonas that may then be used for the efficient conversion of pentose sugars (xylose, arabinose) to ethanol. Method of using the Zymomonas integrants and derivatives thereof in production of ethanol from cellulosic feedstock is also disclosed. The invention also provides a method for preparing a Zymomonas integrant as part of the present invention. The host Zymomonas strain found particularly useful in the creation of these compositions and methods is Zymomonas mobilis 31821.

Linear Lepidopteran ambidensovirus 1 sequences drive random integration of a reporter gene in transfected Spodoptera frugiperda cells.

PubMed

Rizk, Francine; Laverdure, Sylvain; d'Alençon, Emmanuelle; Bossin, Hervé; Dupressoir, Thierry

2018-01-01

The Lepidopteran ambidensovirus 1 isolated from Junonia coenia (hereafter JcDV) is an invertebrate parvovirus considered as a viral transduction vector as well as a potential tool for the biological control of insect pests. Previous works showed that JcDV-based circular plasmids experimentally integrate into insect cells genomic DNA. In order to approach the natural conditions of infection and possible integration, we generated linear JcDV- gfp based molecules which were transfected into non permissive Spodoptera frugiperda ( Sf9 ) cultured cells. Cells were monitored for the expression of green fluorescent protein (GFP) and DNA was analyzed for integration of transduced viral sequences. Non-structural protein modulation of the VP-gene cassette promoter activity was additionally assayed. We show that linear JcDV-derived molecules are capable of long term genomic integration and sustained transgene expression in Sf9 cells. As expected, only the deletion of both inverted terminal repeats (ITR) or the polyadenylation signals of NS and VP genes dramatically impairs the global transduction/expression efficiency. However, all the integrated viral sequences we characterized appear "scrambled" whatever the viral content of the transfected vector. Despite a strong GFP expression, we were unable to recover any full sequence of the original constructs and found rearranged viral and non-viral sequences as well. Cellular flanking sequences were identified as non-coding ones. On the other hand, the kinetics of GFP expression over time led us to investigate the apparent down-regulation by non-structural proteins of the VP-gene cassette promoter. Altogether, our results show that JcDV-derived sequences included in linear DNA molecules are able to drive efficiently the integration and expression of a foreign gene into the genome of insect cells, whatever their composition, provided that at least one ITR is present. However, the transfected sequences were extensively rearranged with cellular DNA during or after random integration in the host cell genome. Lastly, the non-structural proteins seem to participate in the regulation of p9 promoter activity rather than to the integration of viral sequences.

Integrating Science and Technology: Using Technological Pedagogical Content Knowledge as a Framework to Study the Practices of Science Teachers

ERIC Educational Resources Information Center

Pringle, Rose M.; Dawson, Kara; Ritzhaupt, Albert D.

2015-01-01

In this study, we examined how teachers involved in a yearlong technology integration initiative planned to enact technological, pedagogical, and content practices in science lessons. These science teachers, engaged in an initiative to integrate educational technology in inquiry-based science lessons, provided a total of 525 lesson plans for this…

The genesis of craniofacial biology as a health science discipline.

PubMed

Sperber, G H; Sperber, S M

2014-06-01

The craniofacial complex encapsulates the brain and contains the organs for key functions of the body, including sight, hearing and balance, smell, taste, respiration and mastication. All these systems are intimately integrated within the head. The combination of these diverse systems into a new field was dictated by the dental profession's desire for a research branch of basic science devoted and attuned to its specific needs. The traditional subjects of genetics, embryology, anatomy, physiology, biochemistry, dental materials, odontology, molecular biology and palaeoanthropology pertaining to dentistry have been drawn together by many newly emerging technologies. These new technologies include gene sequencing, CAT scanning, MRI imaging, laser scanning, image analysis, ultrasonography, spectroscopy and visualosonics. A vibrant unitary discipline of investigation, craniofacial biology, has emerged that builds on the original concept of 'oral biology' that began in the 1960s. This paper reviews some of the developments that have led to the genesis of craniofacial biology as a fully-fledged health science discipline of significance in the advancement of clinical dental practice. Some of the key figures and milestones in craniofacial biology are identified. © 2014 Australian Dental Association.

Simultaneous Characterization of Somatic Events and HPV-18 Integration in a Metastatic Cervical Carcinoma Patient Using DNA and RNA Sequencing

PubMed Central

Liang, Winnie S.; Aldrich, Jessica; Nasser, Sara; Kurdoglu, Ahmet; Phillips, Lori; Reiman, Rebecca; McDonald, Jacquelyn; Izatt, Tyler; Christoforides, Alexis; Baker, Angela; Craig, Christine; Egan, Jan B.; Chase, Dana M.; Farley, John H.; Bryce, Alan H.; Stewart, A. Keith; Borad, Mitesh J.; Carpten, John D.; Craig, David W.; Monk, Bradley J.

2014-01-01

Objective Integration of carcinogenic human papillomaviruses (HPVs) into the host genome is a significant tumorigenic factor in specific cancers including cervical carcinoma. Although major strides have been made with respect to HPV diagnosis and prevention, identification and development of efficacious treatments for cervical cancer patients remains a goal and thus requires additional detailed characterization of both somatic events and HPV integration. Given this need, the goal of this study was to use the next generation sequencing to simultaneously evaluate somatic alterations and expression changes in a patient’s cervical squamous carcinoma lesion metastatic to the lung and to detect and analyze HPV infection in the same sample. Materials and Methods We performed tumor and normal exome, tumor and normal shallow whole-genome sequencing, and RNA sequencing of the patient’s lung metastasis. Results We generated over 1.2 billion mapped reads and identified 130 somatic point mutations and indels, 21 genic translocations, 16 coding regions demonstrating copy number changes, and over 36 genes demonstrating altered expression in the tumor (corrected P < 0.05). Sequencing also revealed the HPV type 18 (HPV-18) integration in the metastasis. Using both DNA and RNA reads, we pinpointed 3 major events indicating HPV-18 integration into an intronic region of chromosome 6p25.1 in the patient’s tumor and validated these events with Sanger sequencing. This integration site has not been reported for HPV-18. Conclusions We demonstrate that DNA and RNA sequencing can be used to concurrently characterize somatic alterations and expression changes in a biopsy and delineate HPV integration at base resolution in cervical cancer. Further sequencing will allow us to better understand the molecular basis of cervical cancer pathogenesis. PMID:24418928

SigWin-detector: a Grid-enabled workflow for discovering enriched windows of genomic features related to DNA sequences.

PubMed

Inda, Márcia A; van Batenburg, Marinus F; Roos, Marco; Belloum, Adam S Z; Vasunin, Dmitry; Wibisono, Adianto; van Kampen, Antoine H C; Breit, Timo M

2008-08-08

Chromosome location is often used as a scaffold to organize genomic information in both the living cell and molecular biological research. Thus, ever-increasing amounts of data about genomic features are stored in public databases and can be readily visualized by genome browsers. To perform in silico experimentation conveniently with this genomics data, biologists need tools to process and compare datasets routinely and explore the obtained results interactively. The complexity of such experimentation requires these tools to be based on an e-Science approach, hence generic, modular, and reusable. A virtual laboratory environment with workflows, workflow management systems, and Grid computation are therefore essential. Here we apply an e-Science approach to develop SigWin-detector, a workflow-based tool that can detect significantly enriched windows of (genomic) features in a (DNA) sequence in a fast and reproducible way. For proof-of-principle, we utilize a biological use case to detect regions of increased and decreased gene expression (RIDGEs and anti-RIDGEs) in human transcriptome maps. We improved the original method for RIDGE detection by replacing the costly step of estimation by random sampling with a faster analytical formula for computing the distribution of the null hypothesis being tested and by developing a new algorithm for computing moving medians. SigWin-detector was developed using the WS-VLAM workflow management system and consists of several reusable modules that are linked together in a basic workflow. The configuration of this basic workflow can be adapted to satisfy the requirements of the specific in silico experiment. As we show with the results from analyses in the biological use case on RIDGEs, SigWin-detector is an efficient and reusable Grid-based tool for discovering windows enriched for features of a particular type in any sequence of values. Thus, SigWin-detector provides the proof-of-principle for the modular e-Science based concept of integrative bioinformatics experimentation.

Mariner 9 mapping science sequence design.

NASA Technical Reports Server (NTRS)

Goldman, A. M., Jr.

1973-01-01

The primary mission of Mariner 9 was to map the Martian surface. This paper discusses in detail the design of the mapping science sequences which were executed by the spacecraft in sixty days and during which over eighty percent of the surface was photographed. The sequence design was influenced by many factors: experimenter scientific objectives, instrument capabilities, spacecraft capabilities, orbit characteristics, and data return rates, which are illustrated graphically. Typical orbits are depicted for each of the three different mapping phases lasting twenty days. Examples of typical orbital sequence plans prepared daily during mission operations are given.

The Integration of Mathematics in Middle School Science: Student and Teacher Impacts Related to Science Achievement and Attitudes Towards Integration

NASA Astrophysics Data System (ADS)

McHugh, Luisa

Contemporary research has suggested that in order for students to compete globally in the 21st century workplace, pedagogy must shift to include the integration of science and mathematics, where teachers effectively incorporate the two disciplines seamlessly. Mathematics facilitates a deeper understanding of science concepts and has been linked to improved student perception of the integration of science and mathematics. Although there is adequate literature to substantiate students' positive responses to integration in terms of attitudes, there has been little empirical data to support significant academic improvement when both disciplines are taught in an integrated method. This research study, conducted at several school districts on Long Island and New York City, New York, examined teachers' attitudes toward integration and students' attitudes about, and achievement on assessments in, an integrated 8th grade science classroom compared to students in a non-integrated classroom. An examination of these parameters was conducted to analyze the impact of the sizeable investment of time and resources needed to teach an integrated curriculum effectively. These resources included substantial teacher training, planning time, collaboration with colleagues, and administration of student assessments. The findings suggest that students had positive outcomes associated with experiencing an integrated science and mathematics curriculum, though these were only weakly correlated with teacher confidence in implementing the integrated model successfully. The positive outcomes included the ability of students to understand scientific concepts within a concrete mathematical framework, improved confidence in applying mathematics to scientific ideas, and increased agreement with the usefulness of mathematics in interpreting science concepts. Implications of these research findings may be of benefit to educators and policymakers looking to adapt integrated curricula in order to improve the preparation of students to learn and achieve in a global society.

Terragenome: International Soil Metagenome Sequencing Consortium (GSC8 Meeting)

ScienceCinema

Jansson, Janet

2018-01-04

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Janet Jansson of the Lawrence Berkeley National Laboratory discusses the Terragenome Initiative at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.

Developing a heart institute: the execution of a strategic plan.

PubMed

Krawczeski, Catherine D; McDonald, Mark B

2013-01-01

The Heart Institute at Cincinnati Children's Hospital Medical Center was chartered in July 2008 with the purpose of integrating clinical cardiovascular medicine with basic science research to foster innovations in care of patients with congenital heart problems. The initial administrative steering committee included representation from a basic scientist, a cardiologist, and a cardiothoracic surgeon and was charged with the development of a strategic plan for the evolution of the Institute over a five-year horizon. Using structured focus groups and staff interviews, the vision, mission, and goals were identified and refined. An integrated implementation plan addressing recruitment, capitalization, infrastructure, and market opportunities was created and executed. The preliminary results demonstrated clinical outcome improvements, increased scientific and academic productivity, and financial sustainability. All of the goals identified in the initial planning sequence were achieved within the five-year time frame, prompting an early evaluation and revision of the strategic plan.

Integrated view of Vibrio cholerae in the Americas.

PubMed

Domman, Daryl; Quilici, Marie-Laure; Dorman, Matthew J; Njamkepo, Elisabeth; Mutreja, Ankur; Mather, Alison E; Delgado, Gabriella; Morales-Espinosa, Rosario; Grimont, Patrick A D; Lizárraga-Partida, Marcial Leonardo; Bouchier, Christiane; Aanensen, David M; Kuri-Morales, Pablo; Tarr, Cheryl L; Dougan, Gordon; Parkhill, Julian; Campos, Josefina; Cravioto, Alejandro; Weill, François-Xavier; Thomson, Nicholas R

2017-11-10

Latin America has experienced two of the largest cholera epidemics in modern history; one in 1991 and the other in 2010. However, confusion still surrounds the relationships between globally circulating pandemic Vibrio cholerae clones and local bacterial populations. We used whole-genome sequencing to characterize cholera across the Americas over a 40-year time span. We found that both epidemics were the result of intercontinental introductions of seventh pandemic El Tor V. cholerae and that at least seven lineages local to the Americas are associated with disease that differs epidemiologically from epidemic cholera. Our results consolidate historical accounts of pandemic cholera with data to show the importance of local lineages, presenting an integrated view of cholera that is important to the design of future disease control strategies. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Integrating Science and Literacy Instruction: A Framework for Bridging the Gap

ERIC Educational Resources Information Center

Freeman, Gene; Taylor, Vickie

2006-01-01

There is vast research that substantiates the integration of science and literacy; however, there are very few books that correlate findings and address specific practices. "Integrating Science and Literary Instruction" connects scientifically based research and best instructional practices in literacy and integrates this with the inquiry-based…

Preparing prospective physics teachers to teach integrated science in junior high school

NASA Astrophysics Data System (ADS)

Wiyanto; Hartono; Nugroho, S. E.

2018-03-01

The physics education study program especially prepares its students to teach physics in senior high school, however in reality many its graduates have become science teachers in junior high school. Therefore introducing integrated science to prospective physics teachers is important, because based on the curriculum, science in the junior high school should be taught integratedly. This study analyzed integrated science teaching materials that developed by prospective physics teachers. Results from this study showed that majority of the integration materials that developed by the prospective physics teachers focused on topic with an overlapping concept or theme as connecting between two or three subjects.

An instructional package integrating science and social studies instruction at the fifth-grade level

NASA Astrophysics Data System (ADS)

Hulley, Kathy Louise Sullivan

Integrative education is being implemented by classroom teachers who want to immerse students in an environment rich in problem-solving skills, critical analysis skills, ethics, valuing of knowledge, and communication of learning. Several subject areas in the curriculum have been integrated, such as literature with social studies and mathematics with science. The focus of this dissertation is on the integration of science and social studies at the fifth grade level using the Mississippi State Department of Education Curriculum Guidelines and Objectives (MSDE, 1995) and the National Science Education Standards (National Research Council (NRC), 1996). An instructional package of lesson plans that teachers can use as ideas to create their own plans for an integrated curriculum of science and social studies was devised. The Mississippi State Department of Education Curriculum Guidelines and Objectives for Social Studies (MSDE, 1995) at the fifth grade level contain fifteen competencies. Three standards from the National Science Education Standards (NRC, 1996) were chosen. They include (a) science and technology, (b) science in personal and social perspectives, and (c) the history and nature of science. Each competency for social studies has three lesson plans written that integrate the three chosen standards from the National Science Education Standards. A total of forty-five lesson plans were written integrating science and social studies. Each lesson plan includes an objective, materials, procedures, and evaluation for teachers. Teachers are encouraged to use the lesson plans as a guide in creating their own lesson plans that would correspond to their school's particular curriculum guidelines. Consideration should be given to the learning levels and styles of their classroom. This qualitative study was done to create lesson plans that integrate science and social studies with the hope that teachers will expand upon them and implement them into their curricula.

PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities

PubMed Central

2011-01-01

Background Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS) that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. Results The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. Conclusions PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/. PMID:21385349

Super Science Connections.

ERIC Educational Resources Information Center

Smith, Janice, Ed.

This manual was developed to help K-3 teachers incorporate science and science activities as an integral part of their curricula. It integrates hands-on science activities with other curricular areas, particularly the language arts. The activities include science background information, science process skills, classroom management suggestions,…

DNA Sequences from Formalin-Fixed Nematodes: Integrating Molecular and Morphological Approaches to Taxonomy

PubMed Central

Thomas, W. Kelley; Vida, J. T.; Frisse, Linda M.; Mundo, Manuel; Baldwin, James G.

1997-01-01

To effectively integrate DNA sequence analysis and classical nematode taxonomy, we must be able to obtain DNA sequences from formalin-fixed specimens. Microdissected sections of nematodes were removed from specimens fixed in formalin, using standard protocols and without destroying morphological features. The fixed sections provided sufficient template for multiple polymerase chain reaction-based DNA sequence analyses. PMID:19274156

A comparison of students' achievement and attitude as a function of lecture/lab sequencing in a non-science majors introductory biology course

NASA Astrophysics Data System (ADS)

Hurst March, Robin Denise

This investigation compared student achievement and attitudes toward science from three different sequencing approaches used in teaching biology to nonscience students. The three sequencing approaches were the lecture course only, lecture/laboratory courses taken together, and laboratory with previously taken lecture approach. The purposes of this study were to determine if (1) a relationship exists between the Attitude Towards Science in School Assessment (ATSSA) scores (Germann, 1988) and biology achievement, (2) a difference exists among the ATSSA scores and sequencing, (3) a difference exists among the biology achievement scores and sequencing, and (4) the ATSSA is a reliable instrument of science attitude assessment for the undergraduate students in an introductory biology nonmajors laboratory and lecture courses at a research I institution during the fall semester 1996. Fifty-four students comprised the lecture only group, 90 students comprised the lecture and laboratory taken together approach, and 23 students comprised the laboratory only approach. Research questions addressed were (1) What are the differences in student biology achievement as a function of the three different methods of instruction? (2) What are the differences in student attitude towards science as a function of the three different methods of instruction? (3) What is the relationship between post-attitude (ATSSA) and biology achievement for each of the three methods of instruction? An analysis of variance utilized the mean posttest scores on the ATSSA and mean achievement scores as the dependent variables. The independent variables were the three different sequences of enrollment in introductory biology. At the.05 level of significance, it was found that no significant difference existed between the ATTS and laboratory/lecture sequence. At the.05 level of significance, it was found that no significant difference existed between achievement and laboratory/lecture sequence. A Pearson product moment correlation was used to see if a relationship existed between posttest ATSSA scores and achievement totals in each sequence. A significant relationship was noted between the ATSSA and achievement in each sequence that involved a laboratory component.

Golden Ratio Versus Pi as Random Sequence Sources for Monte Carlo Integration

NASA Technical Reports Server (NTRS)

Sen, S. K.; Agarwal, Ravi P.; Shaykhian, Gholam Ali

2007-01-01

We discuss here the relative merits of these numbers as possible random sequence sources. The quality of these sequences is not judged directly based on the outcome of all known tests for the randomness of a sequence. Instead, it is determined implicitly by the accuracy of the Monte Carlo integration in a statistical sense. Since our main motive of using a random sequence is to solve real world problems, it is more desirable if we compare the quality of the sequences based on their performances for these problems in terms of quality/accuracy of the output. We also compare these sources against those generated by a popular pseudo-random generator, viz., the Matlab rand and the quasi-random generator ha/ton both in terms of error and time complexity. Our study demonstrates that consecutive blocks of digits of each of these numbers produce a good random sequence source. It is observed that randomly chosen blocks of digits do not have any remarkable advantage over consecutive blocks for the accuracy of the Monte Carlo integration. Also, it reveals that pi is a better source of a random sequence than theta when the accuracy of the integration is concerned.

Integrating Instruction: Literacy and Science. Tools for Teaching Literacy Series

ERIC Educational Resources Information Center

McKee, Judy; Ogle, Donna

2005-01-01

This book provides a full framework for integrating science and literacy. It shows how tapping into children's interest in science can help them develop key literacy skills and strategies as they explore the world around them. Examples of integrated science units include hands-on instructions and reproducible materials for learning activities that…

Toward an Integrated BAC Library Resource for Genome Sequencing and Analysis

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

Simon, M. I.; Kim, U.-J.

We developed a great deal of expertise in building large BAC libraries from a variety of DNA sources including humans, mice, corn, microorganisms, worms, and Arabidopsis. We greatly improved the technology for screening these libraries rapidly and for selecting appropriate BACs and mapping BACs to develop large overlapping contigs. We became involved in supplying BACs and BAC contigs to a variety of sequencing and mapping projects and we began to collaborate with Drs. Adams and Venter at TIGR and with Dr. Leroy Hood and his group at University of Washington to provide BACs for end sequencing and for mapping andmore » sequencing of large fragments of chromosome 16. Together with Dr. Ian Dunham and his co-workers at the Sanger Center we completed the mapping and they completed the sequencing of the first human chromosome, chromosome 22. This was published in Nature in 1999 and our BAC contigs made a major contribution to this sequencing effort. Drs. Shizuya and Ding invented an automated highly accurate BAC mapping technique. We also developed long-term collaborations with Dr. Uli Weier at UCSF in the design of BAC probes for characterization of human tumors and specific chromosome deletions and breakpoints. Finally the contribution of our work to the human genome project has been recognized in the publication both by the international consortium and the NIH of a draft sequence of the human genome in Nature last year. Dr. Shizuya was acknowledged in the authorship of that landmark paper. Dr. Simon was also an author on the Venter/Adams Celera project sequencing the human genome that was published in Science last year.« less

An efficient and scalable graph modeling approach for capturing information at different levels in next generation sequencing reads

PubMed Central

2013-01-01

Background Next generation sequencing technologies have greatly advanced many research areas of the biomedical sciences through their capability to generate massive amounts of genetic information at unprecedented rates. The advent of next generation sequencing has led to the development of numerous computational tools to analyze and assemble the millions to billions of short sequencing reads produced by these technologies. While these tools filled an important gap, current approaches for storing, processing, and analyzing short read datasets generally have remained simple and lack the complexity needed to efficiently model the produced reads and assemble them correctly. Results Previously, we presented an overlap graph coarsening scheme for modeling read overlap relationships on multiple levels. Most current read assembly and analysis approaches use a single graph or set of clusters to represent the relationships among a read dataset. Instead, we use a series of graphs to represent the reads and their overlap relationships across a spectrum of information granularity. At each information level our algorithm is capable of generating clusters of reads from the reduced graph, forming an integrated graph modeling and clustering approach for read analysis and assembly. Previously we applied our algorithm to simulated and real 454 datasets to assess its ability to efficiently model and cluster next generation sequencing data. In this paper we extend our algorithm to large simulated and real Illumina datasets to demonstrate that our algorithm is practical for both sequencing technologies. Conclusions Our overlap graph theoretic algorithm is able to model next generation sequencing reads at various levels of granularity through the process of graph coarsening. Additionally, our model allows for efficient representation of the read overlap relationships, is scalable for large datasets, and is practical for both Illumina and 454 sequencing technologies. PMID:24564333

BS-virus-finder: virus integration calling using bisulfite sequencing data.

PubMed

Gao, Shengjie; Hu, Xuesong; Xu, Fengping; Gao, Changduo; Xiong, Kai; Zhao, Xiao; Chen, Haixiao; Zhao, Shancen; Wang, Mengyao; Fu, Dongke; Zhao, Xiaohui; Bai, Jie; Mao, Likai; Li, Bo; Wu, Song; Wang, Jian; Li, Shengbin; Yang, Huangming; Bolund, Lars; Pedersen, Christian N S

2018-01-01

DNA methylation plays a key role in the regulation of gene expression and carcinogenesis. Bisulfite sequencing studies mainly focus on calling single nucleotide polymorphism, different methylation region, and find allele-specific DNA methylation. Until now, only a few software tools have focused on virus integration using bisulfite sequencing data. We have developed a new and easy-to-use software tool, named BS-virus-finder (BSVF, RRID:SCR_015727), to detect viral integration breakpoints in whole human genomes. The tool is hosted at https://github.com/BGI-SZ/BSVF. BS-virus-finder demonstrates high sensitivity and specificity. It is useful in epigenetic studies and to reveal the relationship between viral integration and DNA methylation. BS-virus-finder is the first software tool to detect virus integration loci by using bisulfite sequencing data. © The Authors 2017. Published by Oxford University Press.

Examining Curricular Integration Strategies To Optimize Learning Of The Anatomical Sciences

NASA Astrophysics Data System (ADS)

Lisk, Kristina Adriana Ayako

Background: Integration of basic and clinical science knowledge is essential to clinical practice. Although the importance of these two knowledge domains is well-recognized, successfully supporting the development of learners' integrated basic and clinical science knowledge, remains an educational challenge. In this dissertation, I examine curricular integration strategies to optimize learning of the anatomical sciences. Objectives: The studies were designed to achieve the following research aims: 1) to objectively identify clinically relevant content for an integrated musculoskeletal anatomy curriculum; 2) to examine the value of integrated anatomy and clinical science instruction compared to clinical science instruction alone on novices' diagnostic accuracy and diagnostic reasoning process; 3) to compare the effect of integrating and segregating anatomy and clinical science instruction along with a learning strategy (self-explanation) on novices' diagnostic accuracy. Methods: A modified Delphi was used to objectively select clinically relevant content for an integrated musculoskeletal anatomy curriculum. Two experimental studies were created to compare different instructional strategies to optimize learning of the curricular content. In both of these studies, novice learners were taught the clinical features of musculoskeletal pathologies using different learning approaches. Diagnostic performance was measured immediately after instruction and one-week later. Results: The results show that the Delphi method is an effective strategy to select clinically relevant content for integrated anatomy curricula. The findings also demonstrate that novices who were explicitly taught the clinical features of musculoskeletal diseases using causal basic science descriptions had superior diagnostic accuracy and a better understanding of the relative importance of key clinical features for disease categories. Conclusions: This research demonstrates how integration strategies can be applied at multiple levels of the curriculum. Further, this work shows the value of cognitive integration of anatomy and clinical science and it emphasizes the importance of purposefully linking the anatomical and clinical sciences in day-to-day teaching.

Integration of basic sciences and clinical sciences in oral radiology education for dental students.

PubMed

Baghdady, Mariam T; Carnahan, Heather; Lam, Ernest W N; Woods, Nicole N

2013-06-01

Educational research suggests that cognitive processing in diagnostic radiology requires a solid foundation in the basic sciences and knowledge of the radiological changes associated with disease. Although it is generally assumed that dental students must acquire both sets of knowledge, little is known about the most effective way to teach them. Currently, the basic and clinical sciences are taught separately. This study was conducted to compare the diagnostic accuracy of students when taught basic sciences segregated or integrated with clinical features. Predoctoral dental students (n=51) were taught four confusable intrabony abnormalities using basic science descriptions integrated with the radiographic features or taught segregated from the radiographic features. The students were tested with diagnostic images, and memory tests were performed immediately after learning and one week later. On immediate and delayed testing, participants in the integrated basic science group outperformed those from the segregated group. A main effect of learning condition was found to be significant (p<0.05). The results of this study support the critical role of integrating biomedical knowledge in diagnostic radiology and shows that teaching basic sciences integrated with clinical features produces higher diagnostic accuracy in novices than teaching basic sciences segregated from clinical features.

Technology Integration in a Science Classroom: Preservice Teachers' Perceptions

NASA Astrophysics Data System (ADS)

Rehmat, Abeera P.; Bailey, Janelle M.

2014-12-01

The challenge of preparing students for the information age has prompted administrators to increase technology in the public schools. Yet despite the increased availability of technology in schools, few teachers are integrating technology for instructional purposes. Preservice teachers must be equipped with adequate content knowledge of technology to create an advantageous learning experience in science classrooms. To understand preservice teachers' conceptions of technology integration, this research study explored 15 elementary science methods students' definitions of technology and their attitudes toward incorporating technology into their teaching. The phenomenological study took place in a science methods course that was based on a constructivist approach to teaching and learning science through science activities and class discussions, with an emphasis on a teacher beliefs framework. Data were collected throughout the semester, including an open-ended pre/post-technology integration survey, lesson plans, and reflections on activities conducted throughout the course. Through a qualitative analysis, we identified improvements in students' technology definitions, increased technology incorporation into science lesson plans, and favorable attitudes toward technology integration in science teaching after instruction. This research project demonstrates that positive changes in beliefs and behaviors relating to technology integration in science instruction among preservice teachers are possible through explicit instruction.

The Emerging Microbe Project: Developing Clinical Care Plans Based on Pathogen Identification and Clinical Case Studies †

PubMed Central

O’Donnell, Lauren A.; Perry, Michael W.; Doup, Dane’t R.

2015-01-01

For many students in the health sciences, including doctor of pharmacy (PharmD) students, basic and clinical sciences often appear detached from each other. In the infectious disease field, PharmD students additionally struggle with mastering the diversity of microorganisms and the corresponding therapies. The objective of this study was to design an interdisciplinary project that integrates fundamental microbiology with clinical research and decision-making skills. The Emerging Microbe Project guided students through the identification of a microorganism via genetic sequence analysis. The unknown microbe provided the basis for a patient case that asked the student to design a therapeutic treatment strategy for an infected patient. Outside of lecture, students had two weeks to identify the pathogen using nucleotide sequences, compose a microbiology report on the pathogen, and recommend an appropriate therapeutic treatment plan for the corresponding clinical case. We hypothesized that the students would develop a better understanding of the interplay between basic microbiology and infectious disease clinical practice, and that they would gain confidence and skill in independently selecting appropriate antimicrobial therapies for a new disease state. The exercise was conducted with PharmD students in their second professional year of pharmacy school in a required infectious disease course. Here, we demonstrate that the Emerging Microbe Project significantly improved student learning through two assessment strategies (assignment grades and exam questions), and increased student confidence in clinical infectious disease practice. This exercise could be modified for other health sciences students or undergraduates depending upon the level of clinical focus required of the course. PMID:26753029

Authentic Integration: A Model for Integrating Mathematics and Science in the Classroom

ERIC Educational Resources Information Center

Treacy, Páraic; O'Donoghue, John

2014-01-01

Attempts at integrating mathematics and science have been made previously but no definitive, widely adopted teaching model has been developed to date. Research suggests that hands-on, practical, student-centred tasks should form a central element when designing an effective model for the integration of mathematics and science. Aided by this…

Integration of Basic and Clinical Sciences: Faculty Perspectives at a U.S. Dental School.

PubMed

van der Hoeven, Dharini; van der Hoeven, Ransome; Zhu, Liang; Busaidy, Kamal; Quock, Ryan L

2018-04-01

Although dental education has traditionally been organized into basic sciences education (first and second years) and clinical education (third and fourth years), there has been growing interest in ways to better integrate the two to more effectively educate students and prepare them for practice. Since 2012, The University of Texas School of Dentistry at Houston (UTSD) has made it a priority to improve integration of basic and clinical sciences, with a focus to this point on integrating the basic sciences. The aim of this study was to determine the perspectives of basic and clinical science faculty members regarding basic and clinical sciences integration and the degree of integration currently occurring. In October 2016, all 227 faculty members (15 basic scientists and 212 clinicians) were invited to participate in an online survey. Of the 212 clinicians, 84 completed the clinician educator survey (response rate 40%). All 15 basic scientists completed the basic science educator survey (response rate 100%). The majority of basic and clinical respondents affirmed the value of integration (93.3%, 97.6%, respectively) and reported regular integration in their teaching (80%, 86.9%). There were no significant differences between basic scientists and clinicians on perceived importance (p=0.457) and comfort with integration (p=0.240), but the basic scientists were more likely to integrate (p=0.039) and collaborate (p=0.021) than the clinicians. There were no significant differences between generalist and specialist clinicians on importance (p=0.474) and degree (p=0.972) of integration in teaching and intent to collaborate (p=0.864), but the specialists reported feeling more comfortable presenting basic science information (p=0.033). Protected faculty time for collaborative efforts and a repository of integrated basic science and clinical examples for use in teaching and faculty development were recommended to improve integration. Although questions might be raised about the respondents' definition of "integration," this study provides a baseline assessment of perceptions at a dental school that is placing a priority on integration.

Modeling the integration of bacterial rRNA fragments into the human cancer genome.

PubMed

Sieber, Karsten B; Gajer, Pawel; Dunning Hotopp, Julie C

2016-03-21

Cancer is a disease driven by the accumulation of genomic alterations, including the integration of exogenous DNA into the human somatic genome. We previously identified in silico evidence of DNA fragments from a Pseudomonas-like bacteria integrating into the 5'-UTR of four proto-oncogenes in stomach cancer sequencing data. The functional and biological consequences of these bacterial DNA integrations remain unknown. Modeling of these integrations suggests that the previously identified sequences cover most of the sequence flanking the junction between the bacterial and human DNA. Further examination of these reads reveals that these integrations are rich in guanine nucleotides and the integrated bacterial DNA may have complex transcript secondary structures. The models presented here lay the foundation for future experiments to test if bacterial DNA integrations alter the transcription of the human genes.

Interchangeable Positions in Interaction Sequences in Science Classrooms

ERIC Educational Resources Information Center

Rees, Carol; Roth, Wolff-Michael

2017-01-01

Triadic dialogue, the Initiation, Response, Evaluation sequence typical of teacher /student interactions in classrooms, has long been identified as a barrier to students' access to learning, including science learning. A large body of research on the subject has over the years led to projects and policies aimed at increasing opportunities for…

Psychology as an Evolving, Interdisciplinary Science: Integrating Science in Sensation and Perception from Fourier to Fluid Dynamics

ERIC Educational Resources Information Center

Ebersole, Tela M.; Kelty-Stephen, Damian G.

2017-01-01

This article outlines the theoretical rationale and process for an integrated-science approach to teaching sensation and perception (S&P) to undergraduate psychology students that may also serve as an integrated-science curriculum. The course aimed to introduce the interdisciplinary evolution of this psychological field irrespective of any…

Rocking Your Writing Program: Integration of Visual Art, Language Arts, & Science

ERIC Educational Resources Information Center

Poldberg, Monique M.,; Trainin, Guy; Andrzejczak, Nancy

2013-01-01

This paper explores the integration of art, literacy and science in a second grade classroom, showing how an integrative approach has a positive and lasting influence on student achievement in art, literacy, and science. Ways in which art, science, language arts, and cognition intersect are reviewed. Sample artifacts are presented along with their…

An integrated science plan for the Lake Tahoe basin: conceptual framework and research strategies

Treesearch

Zachary P. Hymanson; Michael W. Collopy

2010-01-01

An integrated science plan was developed to identify and refine contemporary science information needs for the Lake Tahoe basin ecosystem. The main objectives were to describe a conceptual framework for an integrated science program, and to develop research strategies addressing key uncertainties and information gaps that challenge government agencies in the theme...

Making Sense of Integrated Science: A Guide for High Schools.

ERIC Educational Resources Information Center

Biological Sciences Curriculum Study, Colorado Springs.

This guide outlines the initial work and includes recommendations for schools and districts on how to implement an integrated science program. Chapters include: (1) "What Is Integrated Science and What Does It Look Like at the High School Level?"; (2) "Coherence in High School Science" (F. James Rutherford); (3) "Thinking about Change: What Will…

Preparation of Nucleic Acid Libraries for Personalized Sequencing Systems Using an Integrated Microfluidic Hub Technology (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

ScienceCinema

Patel, Kamlesh D.

2018-01-22

Kamlesh (Ken) Patel from Sandia National Laboratories (Livermore, California) presents "Preparation of Nucleic Acid Libraries for Personalized Sequencing Systems Using an Integrated Microfluidic Hub Technology " at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

Preparation of Nucleic Acid Libraries for Personalized Sequencing Systems Using an Integrated Microfluidic Hub Technology (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

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

Patel, Kamlesh D.

2012-06-01

Kamlesh (Ken) Patel from Sandia National Laboratories (Livermore, California) presents "Preparation of Nucleic Acid Libraries for Personalized Sequencing Systems Using an Integrated Microfluidic Hub Technology " at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

Students' network integration as a predictor of persistence in introductory physics courses

NASA Astrophysics Data System (ADS)

Zwolak, Justyna P.; Dou, Remy; Williams, Eric A.; Brewe, Eric

2017-06-01

Increasing student retention (successfully finishing a particular course) and persistence (continuing through a sequence of courses or the major area of study) is currently a major challenge for universities. While students' academic and social integration into an institution seems to be vital for student retention, research into the effect of interpersonal interactions is rare. We use network analysis as an approach to investigate academic and social experiences of students in the classroom. In particular, centrality measures identify patterns of interaction that contribute to integration into the university. Using these measures, we analyze how position within a social network in a Modeling Instruction (MI) course—an introductory physics course that strongly emphasizes interactive learning—predicts their persistence in taking a subsequent physics course. Students with higher centrality at the end of the first semester of MI are more likely to enroll in a second semester of MI. Moreover, we found that chances of successfully predicting individual student's persistence based on centrality measures are fairly high—up to 75%, making the centrality a good predictor of persistence. These findings suggest that increasing student social integration may help in improving persistence in science, technology, engineering, and mathematics fields.

Acceleration ground test program to verify GAS payload No. 559 structure/support avionics and experiment structural integrity

NASA Technical Reports Server (NTRS)

Cassanto, John M.; Cassanto, Valerie A.

1988-01-01

Acceleration ground tests were conducted on the Get Away Special (GAS) payload 559 to verify the structural integrity of the structure/support avionics and two of the planned three flight experiments. The ITA (Integrated Test Area) Standardized Experiment Module (ISEM) structure was modified to accommodate the experiments for payload 559. The ISEM avionics consisted of a heavy duty sliver zinc power supply, three orthogonal-mounted low range microgravity accelerometers, a tri-axis high range accelerometer, a solid state recorder/programmer sequencer, and pressure and temperature sensors. The tests were conducted using the Gravitational Plant Physiology Laboratory Centrifuge of the University City Science Center in Philadelphia, PA. The launch-powered flight steady state acceleration profile of the shuttle was simulated from lift-off through jettison of the External Tank (3.0 g's). Additional tests were conducted at twice the nominal powered flight acceleration levels (6 g's) and an over-test condition of four times the powered flight loads to 12.6 g's. The present test program has demonstrated the value of conducting ground tests to verify GAS payload experiment integrity and operation before flying on the shuttle.

Science for the Public Good: Tackling scientific integrity in the federal government

NASA Astrophysics Data System (ADS)

Goldman, G. T.; Halpern, M.; Johnson, C.

2016-12-01

From hydraulic fracturing to climate change to seismic risk, government science and scientists are integral to public decision making in the geosciences. Following calls for increased scientific integrity across the government, policies have been put in place in recent years to be promote transparency and appropriate use of science in government decision making. But how effective have these initiatives been? With the development of scientific integrity policies, new transparency measures, and other efforts in recent years, are we seeing improvements in how federal agencies use science? And importantly, can these safeguards prevent potential future breaches of scientific integrity and misuse science for political gain? Review of recent progress and problems around government scientific integrity, including case studies, policy assessments, and surveys of federal scientists, can shed light on how far the we have come and what areas still need improvement to ensure that government scientific integrity is preserved in the future.

Integration of Basic and Clinical Science in the Psychiatry Clerkship.

PubMed

Wilkins, Kirsten M; Moore, David; Rohrbaugh, Robert M; Briscoe, Gregory W

2017-06-01

Integration of basic and clinical science is a key component of medical education reform, yet best practices have not been identified. The authors compared two methods of basic and clinical science integration in the psychiatry clerkship. Two interventions aimed at integrating basic and clinical science were implemented and compared in a dementia conference: flipped curriculum and coteaching by clinician and physician-scientist. The authors surveyed students following each intervention. Likert-scale responses were compared. Participants in both groups responded favorably to the integration format and would recommend integration be implemented elsewhere in the curriculum. Survey response rates differed significantly between the groups and student engagement with the flipped curriculum video was limited. Flipped curriculum and co-teaching by clinician and physician-scientist are two methods of integrating basic and clinical science in the psychiatry clerkship. Student learning preferences may influence engagement with a particular teaching format.

78 FR 3905 - Center for Scientific Review; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-17

... . Name of Committee: Cardiovascular and Respiratory Sciences Integrated Review Group; Cardiac... 3188, MSC 7808, Bethesda, MD 20892, 301-435- 1146, [email protected] . Name of Committee: Cardiovascular and Respiratory Sciences Integrated Review Group; Clinical and Integrative Cardiovascular Sciences...

Integrating to Learn and Learning to Integrate: A Case Study of an Online Master's Program on Science-Mathematics Integration for Middle School Teachers

ERIC Educational Resources Information Center

Lee, Mimi Miyoung; Chauvot, Jennifer; Plankis, Brian; Vowell, Julie; Culpepper, Shea

2011-01-01

iSMART (Integration of Science, Mathematics, and Reflective Teaching) Program is an online science and mathematics integrated graduate program for middle school teachers across the state of Texas. As part of a large design-based research project, this paper describes the initial stages of the design process of the iSMART program for its first…

77 FR 1932 - Notification of a Public Teleconference of the Science Advisory Board Committee on Science...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-12

... a draft report based on fact-finding activities conducted as part of a study of science integration... Science Advisory Board Committee on Science Integration for Decision Making AGENCY: Environmental Protection Agency (EPA). ACTION: Notice. SUMMARY: The Environmental Protection Agency (EPA or Agency) Science...

Integrated Science: Providing a More Complete Understanding of Complex Problems

USGS Publications Warehouse

,

2006-01-01

Integration among sciences is critical in order to address some of our most pressing problems. Because of the inherent complexity of natural systems, and the increasing complexity of human demands on them, narrowly-focused approaches are no longer sufficient. USGS Workshop on Enhancing Integrated Science, November 1998. The Mid-Continent Geographic Science Center is actively participating in several integrated science studies that include research partners from the other disciplines of the U.S. Geological Survey (USGS), other Federal and State agencies, universities, and private non-government organizations. The following three examples illustrate the diversity of these studies.

Fossil rhabdoviral sequences integrated into arthropod genomes: ontogeny, evolution, and potential functionality.

PubMed

Fort, Philippe; Albertini, Aurélie; Van-Hua, Aurélie; Berthomieu, Arnaud; Roche, Stéphane; Delsuc, Frédéric; Pasteur, Nicole; Capy, Pierre; Gaudin, Yves; Weill, Mylène

2012-01-01

Retroelements represent a considerable fraction of many eukaryotic genomes and are considered major drives for adaptive genetic innovations. Recent discoveries showed that despite not normally using DNA intermediates like retroviruses do, Mononegaviruses (i.e., viruses with nonsegmented, negative-sense RNA genomes) can integrate gene fragments into the genomes of their hosts. This was shown for Bornaviridae and Filoviridae, the sequences of which have been found integrated into the germ line cells of many vertebrate hosts. Here, we show that Rhabdoviridae sequences, the major Mononegavirales family, have integrated only into the genomes of arthropod species. We identified 185 integrated rhabdoviral elements (IREs) coding for nucleoproteins, glycoproteins, or RNA-dependent RNA polymerases; they were mostly found in the genomes of the mosquito Aedes aegypti and the blacklegged tick Ixodes scapularis. Phylogenetic analyses showed that most IREs in A. aegypti derived from multiple independent integration events. Since RNA viruses are submitted to much higher substitution rates as compared with their hosts, IREs thus represent fossil traces of the diversity of extinct Rhabdoviruses. Furthermore, analyses of orthologous IREs in A. aegypti field mosquitoes sampled worldwide identified an integrated polymerase IRE fragment that appeared under purifying selection within several million years, which supports a functional role in the host's biology. These results show that A. aegypti was subjected to repeated Rhabdovirus infectious episodes during its evolution history, which led to the accumulation of many integrated sequences. They also suggest that like retroviruses, integrated rhabdoviral sequences may participate actively in the evolution of their hosts.

DNA methylation at hepatitis B viral integrants is associated with methylation at flanking human genomic sequences

PubMed Central

Watanabe, Yoshiyuki; Yamamoto, Hiroyuki; Oikawa, Ritsuko; Toyota, Minoru; Yamamoto, Masakazu; Kokudo, Norihiro; Tanaka, Shinji; Arii, Shigeki; Yotsuyanagi, Hiroshi; Koike, Kazuhiko; Itoh, Fumio

2015-01-01

Integration of DNA viruses into the human genome plays an important role in various types of tumors, including hepatitis B virus (HBV)–related hepatocellular carcinoma. However, the molecular details and clinical impact of HBV integration on either human or HBV epigenomes are unknown. Here, we show that methylation of the integrated HBV DNA is related to the methylation status of the flanking human genome. We developed a next-generation sequencing-based method for structural methylation analysis of integrated viral genomes (denoted G-NaVI). This method is a novel approach that enables enrichment of viral fragments for sequencing using unique baits based on the sequence of the HBV genome. We detected integrated HBV sequences in the genome of the PLC/PRF/5 cell line and found variable levels of methylation within the integrated HBV genomes. Allele-specific methylation analysis revealed that the HBV genome often became significantly methylated when integrated into highly methylated host sites. After integration into unmethylated human genome regions such as promoters, however, the HBV DNA remains unmethylated and may eventually play an important role in tumorigenesis. The observed dynamic changes in DNA methylation of the host and viral genomes may functionally affect the biological behavior of HBV. These findings may impact public health given that millions of people worldwide are carriers of HBV. We also believe our assay will be a powerful tool to increase our understanding of the various types of DNA virus-associated tumorigenesis. PMID:25653310

A science of integration: frameworks, processes, and products in a place-based, integrative study

USGS Publications Warehouse

Kliskey, Andrew; Alessa, Lilian; Wandersee, Sarah; Williams, Paula; Trammell, Jamie; Powell, Jim; Grunblatt, Jess; Wipfli, Mark S.

2017-01-01

Integrative research is increasingly a priority within the scientific community and is a central goal for the evolving field of sustainability science. While it is conceptually attractive, its successful implementation has been challenging and recent work suggests that the move towards interdisciplinarity and transdisciplinarity in sustainability science is being only partially realized. To address this from the perspective of social-ecological systems (SES) research, we examine the process of conducting a science of integration within the Southcentral Alaska Test Case (SCTC) of Alaska-EPSCoR as a test-bed for this approach. The SCTC is part of a large, 5 year, interdisciplinary study investigating changing environments and adaptations to those changes in Alaska. In this paper, we review progress toward a science of integration and present our efforts to confront the practical issues of applying proposed integration frameworks. We: (1) define our integration framework; (2) describe the collaborative processes, including the co-development of science through stakeholder engagement and partnerships; and (3) illustrate potential products of integrative, social-ecological systems research. The approaches we use can also be applied outside of this particular framework. We highlight challenges and propose improvements for integration in sustainability science by addressing the need for common frameworks and improved contextual understanding. These insights may be useful for capacity-building for interdisciplinary projects that address complex real-world social and environmental problems.

Nanoethics and the breaching of boundaries: a heuristic for going from encouragement to a fuller integration of ethical, legal and social issues and science : commentary on: "Adding to the mix: integrating ELSI into a National Nanoscale Science and Technology Center".

PubMed

Tuma, Julio R

2011-12-01

The intersection of ELSI and science forms a complicated nexus yet their integration is an important goal both for society and for the successful advancement of science. In what follows, I present a heuristic that makes boundary identification and crossing an important tool in the discovery of potential areas of ethical, legal, and social concern in science. A dynamic and iterative application of the heuristic can lead towards a fuller integration and appreciation of the concerns of ELSI and of science from both sides of the divide.

An analysis of integrated science and language arts themes in software at the elementary school level

NASA Astrophysics Data System (ADS)

Libidinsky, Lisa Jill

2002-09-01

There are many demands on the elementary classroom teacher today, such that teachers often do not have the time and resources to instruct in a meaningful manner that would produce effective, real instruction. Subjects are often disjointed and not significant. When teachers instruct using an integrated approach, students learn more efficiently as they see connections in the subjects. Science and language arts, when combined to produce an integrated approach, show positive associations that can enable students to learn real-life connections. In addition, with the onset of technology and the increased usage of technological programs in the schools, teachers can use technology to support an integrated curriculum. When teachers use a combined instructional focus of science, language arts, and technology to produce lessons, students are able to gain knowledge of concepts and skills necessary for appropriate academic growth and development. Given that there are many software programs available to teachers for classroom use, it is imperative that quality software is used for instruction. Using criteria based upon an intensive literature review of integrated instruction in the areas of science and language arts, this study examines science and language arts software programs to determine whether there are science and language arts integrated themes in the software analyzed. Also, this study examines whether more science and language arts integrated themes are present in science or language arts software programs. Overall, this study finds a significant difference between language arts software and science software when looking at integrated themes. This study shows that science software shows integrated themes with language arts more often than does language arts software with science. The findings in this study can serve as a reference point for educators when selecting software that is meaningful and effective in the elementary classroom. Based on this study, it is apparent that there is a need to evaluate software for appropriate use in the classroom in order to promote effective education.

From proteomics to systems biology: MAPA, MASS WESTERN, PROMEX, and COVAIN as a user-oriented platform.

PubMed

Weckwerth, Wolfram; Wienkoop, Stefanie; Hoehenwarter, Wolfgang; Egelhofer, Volker; Sun, Xiaoliang

2014-01-01

Genome sequencing and systems biology are revolutionizing life sciences. Proteomics emerged as a fundamental technique of this novel research area as it is the basis for gene function analysis and modeling of dynamic protein networks. Here a complete proteomics platform suited for functional genomics and systems biology is presented. The strategy includes MAPA (mass accuracy precursor alignment; http://www.univie.ac.at/mosys/software.html ) as a rapid exploratory analysis step; MASS WESTERN for targeted proteomics; COVAIN ( http://www.univie.ac.at/mosys/software.html ) for multivariate statistical analysis, data integration, and data mining; and PROMEX ( http://www.univie.ac.at/mosys/databases.html ) as a database module for proteogenomics and proteotypic peptides for targeted analysis. Moreover, the presented platform can also be utilized to integrate metabolomics and transcriptomics data for the analysis of metabolite-protein-transcript correlations and time course analysis using COVAIN. Examples for the integration of MAPA and MASS WESTERN data, proteogenomic and metabolic modeling approaches for functional genomics, phosphoproteomics by integration of MOAC (metal-oxide affinity chromatography) with MAPA, and the integration of metabolomics, transcriptomics, proteomics, and physiological data using this platform are presented. All software and step-by-step tutorials for data processing and data mining can be downloaded from http://www.univie.ac.at/mosys/software.html.

Computational prediction of over-annotated protein-coding genes in the genome of Agrobacterium tumefaciens strain C58

NASA Astrophysics Data System (ADS)

Yu, Jia-Feng; Sui, Tian-Xiang; Wang, Hong-Mei; Wang, Chun-Ling; Jing, Li; Wang, Ji-Hua

2015-12-01

Agrobacterium tumefaciens strain C58 is a type of pathogen that can cause tumors in some dicotyledonous plants. Ever since the genome of A. tumefaciens strain C58 was sequenced, the quality of annotation of its protein-coding genes has been queried continually, because the annotation varies greatly among different databases. In this paper, the questionable hypothetical genes were re-predicted by integrating the TN curve and Z curve methods. As a result, 30 genes originally annotated as “hypothetical” were discriminated as being non-coding sequences. By testing the re-prediction program 10 times on data sets composed of the function-known genes, the mean accuracy of 99.99% and mean Matthews correlation coefficient value of 0.9999 were obtained. Further sequence analysis and COG analysis showed that the re-annotation results were very reliable. This work can provide an efficient tool and data resources for future studies of A. tumefaciens strain C58. Project supported by the National Natural Science Foundation of China (Grant Nos. 61302186 and 61271378) and the Funding from the State Key Laboratory of Bioelectronics of Southeast University.

Science Opportunity Analyzer (SOA): Not Just Another Pretty Face

NASA Technical Reports Server (NTRS)

Polanskey, Carol A.; Streiiffert, Barbara; O'Reilly, Taifun

2004-01-01

This viewgraph presentation reviews the Science Opportunity Analyzer (SOA). For the first time at JPL, the Cassini mission to Saturn is using distributed science operations for sequence generation. This means that scientist at other institutions has more responsibility to build the spacecraft sequence. Tools are required to support the sequence development. JPL tools required a complete configuration behind a firewall, and the tools that the user community had developed did not interface with the JPL tools. Therefore the SOA was created to bridge the gap between the remote scientists and the JPL operations teams. The presentation reviews the development of the SOA, and what was required of the system. The presentation reviews the functions that the SOA performed.

75 FR 20843 - Notice of Workshop To Discuss Policy-Relevant Science to Inform EPA's Integrated Plan for the...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-21

... Policy-Relevant Science to Inform EPA's Integrated Plan for the Review of the Lead National Ambient Air...-Relevant Science to Inform EPA's Integrated Plan for Review of the National Ambient Air Quality Standards... review focuses on the key policy-relevant issues and considers the most meaningful new science to inform...

The Integration of Mathematics in Middle School Science: Student and Teacher Impacts Related to Science Achievement and Attitudes towards Integration

ERIC Educational Resources Information Center

McHugh, Luisa

2016-01-01

Contemporary research has suggested that in order for students to compete globally in the 21st century workplace, pedagogy must shift to include the integration of science and mathematics, where teachers effectively incorporate the two disciplines seamlessly. Mathematics facilitates a deeper understanding of science concepts and has been linked to…

Topographic Science

USGS Publications Warehouse

Poppenga, Sandra K.; Evans, Gayla; Gesch, Dean; Stoker, Jason M.; Queija, Vivian R.; Worstell, Bruce; Tyler, Dean J.; Danielson, Jeff; Bliss, Norman; Greenlee, Susan

2010-01-01

The mission of U.S. Geological Survey (USGS) Earth Resources Observation and Science (EROS) Center Topographic Science is to establish partnerships and conduct research and applications that facilitate the development and use of integrated national and global topographic datasets. Topographic Science includes a wide range of research and applications that result in improved seamless topographic datasets, advanced elevation technology, data integration and terrain visualization, new and improved elevation derivatives, and development of Web-based tools. In cooperation with our partners, Topographic Science is developing integrated-science applications for mapping, national natural resource initiatives, hazards, and global change science. http://topotools.cr.usgs.gov/.

An Integrated Physical, Genetic and Cytogenetic Map of Brachypodium distachyon, a Model System for Grass Research

PubMed Central

Febrer, Melanie; Goicoechea, Jose Luis; Wright, Jonathan; McKenzie, Neil; Song, Xiang; Lin, Jinke; Collura, Kristi; Wissotski, Marina; Yu, Yeisoo; Ammiraju, Jetty S. S.; Wolny, Elzbieta; Idziak, Dominika; Betekhtin, Alexander; Kudrna, Dave; Hasterok, Robert; Wing, Rod A.; Bevan, Michael W.

2010-01-01

The pooid subfamily of grasses includes some of the most important crop, forage and turf species, such as wheat, barley and Lolium. Developing genomic resources, such as whole-genome physical maps, for analysing the large and complex genomes of these crops and for facilitating biological research in grasses is an important goal in plant biology. We describe a bacterial artificial chromosome (BAC)-based physical map of the wild pooid grass Brachypodium distachyon and integrate this with whole genome shotgun sequence (WGS) assemblies using BAC end sequences (BES). The resulting physical map contains 26 contigs spanning the 272 Mb genome. BES from the physical map were also used to integrate a genetic map. This provides an independent vaildation and confirmation of the published WGS assembly. Mapped BACs were used in Fluorescence In Situ Hybridisation (FISH) experiments to align the integrated physical map and sequence assemblies to chromosomes with high resolution. The physical, genetic and cytogenetic maps, integrated with whole genome shotgun sequence assemblies, enhance the accuracy and durability of this important genome sequence and will directly facilitate gene isolation. PMID:20976139

Asset - An application in mission automation for science planning

NASA Technical Reports Server (NTRS)

Finnerty, D. F.; Martin, J.; Doms, P. E.

1987-01-01

Recent advances in computer technology were used to great advantage in planning science observation sequences for the Voyager 2 encounter with Uranus in 1986. Despite a loss of experienced personnel, a challenging schedule, workforce limitations, and the complex nature of the Uranus encounter itself, the resultant science observation timelines were the most highly optimized of the five Voyager encounters with the outer planets. In part, this was due to the development of a microcomputer-based system, called ASSET (Automated Science Sequence Encounter Timelines generator), which was used to design those science observation timelines. This paper details the development of that system. ASSET demonstrates several features essential to the design of the first expert systems for science planning which will be applied for future missions.

Biological data sciences in genome research

PubMed Central

Schatz, Michael C.

2015-01-01

The last 20 years have been a remarkable era for biology and medicine. One of the most significant achievements has been the sequencing of the first human genomes, which has laid the foundation for profound insights into human genetics, the intricacies of regulation and development, and the forces of evolution. Incredibly, as we look into the future over the next 20 years, we see the very real potential for sequencing more than 1 billion genomes, bringing even deeper insight into human genetics as well as the genetics of millions of other species on the planet. Realizing this great potential for medicine and biology, though, will only be achieved through the integration and development of highly scalable computational and quantitative approaches that can keep pace with the rapid improvements to biotechnology. In this perspective, I aim to chart out these future technologies, anticipate the major themes of research, and call out the challenges ahead. One of the largest shifts will be in the training used to prepare the class of 2035 for their highly interdisciplinary world. PMID:26430150

A Network for Integrated Science and Mathematics Teaching and Learning Conference Plenary Papers. NSF/SSMA Wingspread Conference (Racine, Wisconsin, April 1991). School Science and Mathematics Association Topics for Teachers Series Number 7.

ERIC Educational Resources Information Center

Berlin, Donna F., Ed.

The integration of mathematics and science is not a new concept. However, during recent years it has been a major focus in education reform. A Wingspread conference promoted discussion regarding the integration of mathematics and science and explored ways to improve science and mathematics education in grades K-12. Papers from the conference…

Enhancing Elementary Students' Experiences Learning about Circuits Using an Exploration-Explanation Instructional Sequence

ERIC Educational Resources Information Center

Brown, Timothy M.; Brown, Patrick L.

2010-01-01

Using an exploration-explanation sequence of science instruction helps teachers unveil students' prior knowledge about circuits and engage them in minds-on science learning. In these lessons, fourth grade students make predictions and test their ideas about circuits in series through hands-on investigations. The teacher helps students make…

Evolution in a Test Tube: Exploring the Structure and Function of RNA Probes

DTIC Science & Technology

2008-05-02

Bartel, D.P. and Szostak, J.W. (1993) Isolation of New Ribozymes from a Large Pool of Random Sequences. Science, New Series 261, 1141-1418. 24...Szostak, J.W. (1993) Isolation of New Ribozymes from a Large Pool of Random Sequences. Science, New Series 261, 1141-1418. Chen, Ying; Carlini

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

ERIC Educational Resources Information Center

Wiebke, Heidi; Park Rogers, Meredith

2014-01-01

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

Life science payloads planning study integration facility survey results

NASA Technical Reports Server (NTRS)

Wells, G. W.; Brown, N. E.; Nelson, W. G.

1976-01-01

The integration facility survey effort described is structured to examine the facility resources needed to conduct life science payload (LSP) integration checkout activities at NASA-JSC. The LSP integration facility operations and functions are defined along with the LSP requirements for facility design. A description of available JSC life science facilities is presented and a comparison of accommodations versus requirements is reported.

A Glance at Microsatellite Motifs from 454 Sequencing Reads of Watermelon Genomic DNA

USDA-ARS?s Scientific Manuscript database

A single 454 (Life Sciences Sequencing Technology) run of Charleston Gray watermelon (Citrullus lanatus var. lanatus) genomic DNA was performed and sequence data were assembled. A large scale identification of simple sequence repeat (SSR) was performed and SSR sequence data were used for the develo...

Materials for Integrating Science and Social Studies with the Language Arts (Instructional Resources).

ERIC Educational Resources Information Center

Spiegel, Dixie Lee

1990-01-01

Discusses evaluating resources for integrating science and social studies with the language arts by using questions that teacher-reviewers used when evaluating those resources. Reviews trade books and other resources designed for the integration of science and social studies. (MG)

Preamble to the Integrated Science Assessments (ISA)

EPA Science Inventory

The Preamble to the Integrated Science Assessments, or "Preamble", is an overview document outlining the basic steps and criteria used in developing the Integrated Science Assessments (ISA). Previously included as part of the ISA, it will now be referenced by each ISA as...

Evaluation of Seeds of Science/Roots of Reading Project: "Shoreline Science" and "Terrarium Investigations." CSE Technical Report 676

ERIC Educational Resources Information Center

Wang, Jia; Baker, Eva L.

2006-01-01

This project was initiated in order to evaluate two literacy and science integrated instruction units, "Shoreline Science" and "Terrarium Investigations," designed by the Lawrence Hall of Science "Seeds of Science/Roots of Reading" Project ("Seeds/Roots"). We examined how the integrated units affect student…

76 FR 13182 - Science Advisory Board Staff Office; Notification of a Public Meeting of the Science Advisory...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-10

... results of fact-finding activities conducted as part of a study of science integration supporting EPA... ENVIRONMENTAL PROTECTION AGENCY [FRL-9278-1] Science Advisory Board Staff Office; Notification of a Public Meeting of the Science Advisory Board Committee on Science Integration for Decision Making...

Cognition before curriculum: rethinking the integration of basic science and clinical learning.

PubMed

Kulasegaram, Kulamakan Mahan; Martimianakis, Maria Athina; Mylopoulos, Maria; Whitehead, Cynthia R; Woods, Nicole N

2013-10-01

Integrating basic science and clinical concepts in the undergraduate medical curriculum is an important challenge for medical education. The health professions education literature includes a variety of educational strategies for integrating basic science and clinical concepts at multiple levels of the curriculum. To date, assessment of this literature has been limited. In this critical narrative review, the authors analyzed literature published in the last 30 years (1982-2012) using a previously published integration framework. They included studies that documented approaches to integration at the level of programs, courses, or teaching sessions and that aimed to improve learning outcomes. The authors evaluated these studies for evidence of successful integration and to identify factors that contribute to integration. Several strategies at the program and course level are well described but poorly evaluated. Multiple factors contribute to successful learning, so identifying how interventions at these levels result in successful integration is difficult. Evidence from session-level interventions and experimental studies suggests that integration can be achieved if learning interventions attempt to link basic and clinical science in a causal relationship. These interventions attend to how learners connect different domains of knowledge and suggest that successful integration requires learners to build cognitive associations between basic and clinical science. One way of understanding the integration of basic and clinical science is as a cognitive activity occurring within learners. This perspective suggests that learner-centered, content-focused, and session-level-oriented strategies can achieve cognitive integration.

Helicos BioSciences.

PubMed

Milos, Patrice

2008-04-01

Helicos BioSciences Corporation is a life sciences company developing revolutionary new single molecule sequencing technology to provide the path to the US$1000 genome. True Single Molecule Sequencing (tSMS) will drive advancements in pharmacogenomics that can enable a better understanding of an individual's susceptibility to disease, develop more effective disease diagnoses and differentiate response to disease therapies. During 2007, genome-wide disease-association studies, the encylopedia of DNA elements (ENCODE) and the published genome sequence of two individuals have revealed human genome variation far more extensive than originally believed. These also demonstrated that common variations explain only a fraction of the genetic basis of disease. Therefore, the capability to understand an individual genome is critical in setting the foundation for the next great revolution in healthcare. Helicos is committed to this vision and will provide cost-effective genome sequencing and comprehensive analysis of the transcribed genome that can unlock the era of personalized healthcare.

The use of FTA cards for transport and detection of gyrA mutation of Campylobacter jejuni from poultry.

PubMed

Sierra-Arguello, Y M; Faulkner, O; Tellez, G; Hargis, B M; Pinheiro do Nascimento, V

2016-04-01

The purpose of the present study was to evaluate a technique involving the use of commercially available FTA classic card (Whatman) for transporting and detection of DNA to use in PCR analysis and genetic sequencing of Campylobacter jejuni of poultry origin. Fifty isolates of Campylobacter jejuni were obtained from broiler carcasses in Rio Grande do Sul, Brazil. Antimicrobial susceptibility testing to ciprofloxacin revealed that all 50 isolates were resistant to ciprofloxacin. Each isolate was transferred to Brucella broth tubes and incubated overnight at 41.5°C. Cell cultures were diluted to match a McFarland Turbidity Standard 0.5, and 110 μL of the cell suspension were applied to one circle on Whatman FTA classic cards. The samples were then covered and allowed to dry at room temperature. Cards were identified and stored at room temperature until further use (3 mo after collection). FTA cards were shipped for analysis to the Department of Poultry Science, University of Arkansas. Amplification of the Campylobacter gyrA gene was successful and demonstrated strong bands for a large amplicon for all 50 samples preserved on FTA cards. Mutations present in each gene were confirmed by DNA sequencing. Then, 7 samples were chosen for the sequencing. The detection of a mutation regarding ciprofloxacin-resistant isolates revealed that 7 samples had a mutation in the gyrA gene. In conclusion, the characteristics of the profiles suggest that the DNA has maintained its integrity after 3 mo of storage at room temperature and is a suitable template for PCR and sequencing from Campylobacter samples. The application of this technology has potential in numerous methodologies, especially when working in remote areas and in developing countries where access to laboratory facilities and equipment is limited. © 2016 Poultry Science Association Inc.

Teachers' Organization of Participation Structures for Teaching Science with Computer Technology

NASA Astrophysics Data System (ADS)

Subramaniam, Karthigeyan

2016-08-01

This paper describes a qualitative study that investigated the nature of the participation structures and how the participation structures were organized by four science teachers when they constructed and communicated science content in their classrooms with computer technology. Participation structures focus on the activity structures and processes in social settings like classrooms thereby providing glimpses into the complex dynamics of teacher-students interactions, configurations, and conventions during collective meaning making and knowledge creation. Data included observations, interviews, and focus group interviews. Analysis revealed that the dominant participation structure evident within participants' instruction with computer technology was ( Teacher) initiation-( Student and Teacher) response sequences-( Teacher) evaluate participation structure. Three key events characterized the how participants organized this participation structure in their classrooms: setting the stage for interactive instruction, the joint activity, and maintaining accountability. Implications include the following: (1) teacher educators need to tap into the knowledge base that underscores science teachers' learning to teach philosophies when computer technology is used in instruction. (2) Teacher educators need to emphasize the essential idea that learning and cognition is not situated within the computer technology but within the pedagogical practices, specifically the participation structures. (3) The pedagogical practices developed with the integration or with the use of computer technology underscored by the teachers' own knowledge of classroom contexts and curriculum needs to be the focus for how students learn science content with computer technology instead of just focusing on how computer technology solely supports students learning of science content.

The influence of a train-the-trainer professional development on teacher perceptions of science integration and inquiry-based instruction

NASA Astrophysics Data System (ADS)

Blythe, Jessica Marie

The purpose of this study was to describe the influence of the train-the-trainer professional development form of professional development on participants' perceptions of agriscience integration and inquiry-based instruction (IBI). The independent variables considered were elements of high-quality professional development, such as duration, active participation, coherence, and school culture; teacher attitudes towards professional development; and teacher demographics. The dependent variables assessed were teachers' perceptions of agriscience integration and IBI. This study utilized a quasi-experimental design to assess the impacts of a teacher professional development program and experimental follow-up support on secondary teachers' perceptions of science integration and IBI. This study was a census of all teachers who attended a 2012 professional development workshop facilitated by a National Agriscience Teacher Ambassador at the FFA and/or NAAE National Convention. Participants completed four surveys over the subsequent year to assess their perceptions of agriscience integration and IBI. Descriptive methods were used to analyze teachers' perceptions of agriscience integration and IBI. Correlations and follow-up regression analysis were conducted to determine the relationships between the teachers' perceptions and the elements of high-quality teacher professional development. Results of the study revealed that respondents had favorable perceptions of science integration into agriculture programs and planned to increase the levels of science integration in their programs. Additionally, a majority of respondents reported utilizing IBI more than once a week. Because participants of the study did not utilize the experimental follow-up support system for the workshop, clear effects could not be determined. There was a positive correlation between science integration and IBI. A variation of positive and negative correlations was found between the dependent and independent variables. Five models were found to be significant predictors of respondents' perceptions of science integration three models were found to be significant predictors of IBI. These findings indicate that teachers perceive science integration and IBI as positive influences in secondary agriculture education which supports the integration of science and science teaching techniques in secondary agriculture education programs. Though relationships exist between science integration and IBI, and various elements of school culture and professional development, further investigation is needed to better understand these relationships and their predictive variability.

The Effect of an Integrated Science and Mathematics Content-Based Course on Science and Mathematics Teaching Efficacy of Preservice Elementary Teachers

ERIC Educational Resources Information Center

Moseley, Christine; Utley, Juliana

2006-01-01

The purpose of this study was to determine the effect of an earth systems science course (integrated mathematics and science content) on preservice elementary teachers' mathematics and science teaching efficacy. Paired t-tests revealed that the personal mathematics and science teaching efficacy and science teaching outcome expectancy significantly…

The implementation of integrated science teaching materials based socio-scientific issues to improve students scientific literacy for environmental pollution theme

NASA Astrophysics Data System (ADS)

Yenni, Rita; Hernani, Widodo, Ari

2017-05-01

The study aims to determine the increasing of students' science literacy skills on content aspects and competency of science by using Integrated Science teaching materials based Socio-scientific Issues (SSI) for environmental pollution theme. The method used in the study is quasi-experiment with nonequivalent pretest and posttest control group design. The students of experimental class used teaching materials based SSI, whereas the students of control class were still using the usual textbooks. The result of this study showed a significant difference between the value of N-gain of experimental class and control class, whichalso occurred in every indicator of content aspects and competency of science. This result indicates that using of Integrated Science teaching materials based SSI can improve content aspect and competency of science and can be used as teaching materials alternative in teaching of Integrated Science.

From PCK to TPACK: Developing a Transformative Model for Pre-Service Science Teachers

NASA Astrophysics Data System (ADS)

Jang, Syh-Jong; Chen, Kuan-Chung

2010-12-01

New science teachers should be equipped with the ability to integrate and design the curriculum and technology for innovative teaching. How to integrate technology into pre-service science teachers' pedagogical content knowledge is the important issue. This study examined the impact on a transformative model of integrating technology and peer coaching for developing technological pedagogical and content knowledge (TPACK) of pre-service science teachers. A transformative model and an online system were designed to restructure science teacher education courses. Participants of this study included an instructor and 12 pre-service teachers. The main sources of data included written assignments, online data, reflective journals, videotapes and interviews. This study expanded four views, namely, the comprehensive, imitative, transformative and integrative views to explore the impact of TPACK. The model could help pre-service teachers develop technological pedagogical methods and strategies of integrating subject-matter knowledge into science lessons, and further enhanced their TPACK.

Integration and timing of basic and clinical sciences education.

PubMed

Bandiera, Glen; Boucher, Andree; Neville, Alan; Kuper, Ayelet; Hodges, Brian

2013-05-01

Medical education has traditionally been compartmentalized into basic and clinical sciences, with the latter being viewed as the skillful application of the former. Over time, the relevance of basic sciences has become defined by their role in supporting clinical problem solving rather than being, of themselves, a defining knowledge base of physicians. As part of the national Future of Medical Education in Canada (FMEC MD) project, a comprehensive empirical environmental scan identified the timing and integration of basic sciences as a key pressing issue for medical education. Using the literature review, key informant interviews, stakeholder meetings, and subsequent consultation forums from the FMEC project, this paper details the empirical basis for focusing on the role of basic science, the evidentiary foundations for current practices, and the implications for medical education. Despite a dearth of definitive relevant studies, opinions about how best to integrate the sciences remain strong. Resource allocation, political power, educational philosophy, and the shift from a knowledge-based to a problem-solving profession all influence the debate. There was little disagreement that both sciences are important, that many traditional models emphasized deep understanding of limited basic science disciplines at the expense of other relevant content such as social sciences, or that teaching the sciences contemporaneously rather than sequentially has theoretical and practical merit. Innovations in integrated curriculum design have occurred internationally. Less clear are the appropriate balance of the sciences, the best integration model, and solutions to the political and practical challenges of integrated curricula. New curricula tend to emphasize integration, development of more diverse physician competencies, and preparation of physicians to adapt to evolving technology and patients' expectations. Refocusing the basic/clinical dichotomy to a foundational/applied model may yield benefits in training widely competent future physicians.

ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data.

PubMed

Luo, Guan-Zheng; Yang, Wei; Ma, Ying-Ke; Wang, Xiu-Jie

2014-02-01

Integrative Short Reads NAvigator (ISRNA) is an online toolkit for analyzing high-throughput small RNA sequencing data. Besides the high-speed genome mapping function, ISRNA provides statistics for genomic location, length distribution and nucleotide composition bias analysis of sequence reads. Number of reads mapped to known microRNAs and other classes of short non-coding RNAs, coverage of short reads on genes, expression abundance of sequence reads as well as some other analysis functions are also supported. The versatile search functions enable users to select sequence reads according to their sub-sequences, expression abundance, genomic location, relationship to genes, etc. A specialized genome browser is integrated to visualize the genomic distribution of short reads. ISRNA also supports management and comparison among multiple datasets. ISRNA is implemented in Java/C++/Perl/MySQL and can be freely accessed at http://omicslab.genetics.ac.cn/ISRNA/.

Ozone (O3) Standards - Integrated Science Assessments from Current Review

EPA Pesticide Factsheets

The integrated science assessment (ISA) is a comprehensive review, synthesis, and evaluation of the most policy-relevant science, including key science judgments that are important to inform the development of the risk and exposure assessments, and more.

Mix It Up

ERIC Educational Resources Information Center

Vasquez-Mireles, Selina; West, Sandra

2007-01-01

A correlated science lesson is characterized as an integrated science lesson in that it may incorporate traditionally integrated activities and use math as a tool. However, a correlated math-science lesson also: (1) has the pertinent math and science objectives aligned with state standards; and (2) teaches parallel science and math ideas equally.…

Integration of bioinformatics into an undergraduate biology curriculum and the impact on development of mathematical skills.

PubMed

Wightman, Bruce; Hark, Amy T

2012-01-01

The development of fields such as bioinformatics and genomics has created new challenges and opportunities for undergraduate biology curricula. Students preparing for careers in science, technology, and medicine need more intensive study of bioinformatics and more sophisticated training in the mathematics on which this field is based. In this study, we deliberately integrated bioinformatics instruction at multiple course levels into an existing biology curriculum. Students in an introductory biology course, intermediate lab courses, and advanced project-oriented courses all participated in new course components designed to sequentially introduce bioinformatics skills and knowledge, as well as computational approaches that are common to many bioinformatics applications. In each course, bioinformatics learning was embedded in an existing disciplinary instructional sequence, as opposed to having a single course where all bioinformatics learning occurs. We designed direct and indirect assessment tools to follow student progress through the course sequence. Our data show significant gains in both student confidence and ability in bioinformatics during individual courses and as course level increases. Despite evidence of substantial student learning in both bioinformatics and mathematics, students were skeptical about the link between learning bioinformatics and learning mathematics. While our approach resulted in substantial learning gains, student "buy-in" and engagement might be better in longer project-based activities that demand application of skills to research problems. Nevertheless, in situations where a concentrated focus on project-oriented bioinformatics is not possible or desirable, our approach of integrating multiple smaller components into an existing curriculum provides an alternative. Copyright © 2012 Wiley Periodicals, Inc.

An integrated SNP mining and utilization (ISMU) pipeline for next generation sequencing data.

PubMed

Azam, Sarwar; Rathore, Abhishek; Shah, Trushar M; Telluri, Mohan; Amindala, BhanuPrakash; Ruperao, Pradeep; Katta, Mohan A V S K; Varshney, Rajeev K

2014-01-01

Open source single nucleotide polymorphism (SNP) discovery pipelines for next generation sequencing data commonly requires working knowledge of command line interface, massive computational resources and expertise which is a daunting task for biologists. Further, the SNP information generated may not be readily used for downstream processes such as genotyping. Hence, a comprehensive pipeline has been developed by integrating several open source next generation sequencing (NGS) tools along with a graphical user interface called Integrated SNP Mining and Utilization (ISMU) for SNP discovery and their utilization by developing genotyping assays. The pipeline features functionalities such as pre-processing of raw data, integration of open source alignment tools (Bowtie2, BWA, Maq, NovoAlign and SOAP2), SNP prediction (SAMtools/SOAPsnp/CNS2snp and CbCC) methods and interfaces for developing genotyping assays. The pipeline outputs a list of high quality SNPs between all pairwise combinations of genotypes analyzed, in addition to the reference genome/sequence. Visualization tools (Tablet and Flapjack) integrated into the pipeline enable inspection of the alignment and errors, if any. The pipeline also provides a confidence score or polymorphism information content value with flanking sequences for identified SNPs in standard format required for developing marker genotyping (KASP and Golden Gate) assays. The pipeline enables users to process a range of NGS datasets such as whole genome re-sequencing, restriction site associated DNA sequencing and transcriptome sequencing data at a fast speed. The pipeline is very useful for plant genetics and breeding community with no computational expertise in order to discover SNPs and utilize in genomics, genetics and breeding studies. The pipeline has been parallelized to process huge datasets of next generation sequencing. It has been developed in Java language and is available at http://hpc.icrisat.cgiar.org/ISMU as a standalone free software.

Improving membrane protein expression by optimizing integration efficiency

PubMed Central

2017-01-01

The heterologous overexpression of integral membrane proteins in Escherichia coli often yields insufficient quantities of purifiable protein for applications of interest. The current study leverages a recently demonstrated link between co-translational membrane integration efficiency and protein expression levels to predict protein sequence modifications that improve expression. Membrane integration efficiencies, obtained using a coarse-grained simulation approach, robustly predicted effects on expression of the integral membrane protein TatC for a set of 140 sequence modifications, including loop-swap chimeras and single-residue mutations distributed throughout the protein sequence. Mutations that improve simulated integration efficiency were 4-fold enriched with respect to improved experimentally observed expression levels. Furthermore, the effects of double mutations on both simulated integration efficiency and experimentally observed expression levels were cumulative and largely independent, suggesting that multiple mutations can be introduced to yield higher levels of purifiable protein. This work provides a foundation for a general method for the rational overexpression of integral membrane proteins based on computationally simulated membrane integration efficiencies. PMID:28918393

Retroviral DNA Integration Directed by HIV Integration Protein in Vitro

NASA Astrophysics Data System (ADS)

Bushman, Frederic D.; Fujiwara, Tamio; Craigie, Robert

1990-09-01

Efficient retroviral growth requires integration of a DNA copy of the viral RNA genome into a chromosome of the host. As a first step in analyzing the mechanism of integration of human immunodeficiency virus (HIV) DNA, a cell-free system was established that models the integration reaction. The in vitro system depends on the HIV integration (IN) protein, which was partially purified from insect cells engineered to express IN protein in large quantities. Integration was detected in a biological assay that scores the insertion of a linear DNA containing HIV terminal sequences into a λ DNA target. Some integration products generated in this assay contained five-base pair duplications of the target DNA at the recombination junctions, a characteristic of HIV integration in vivo; the remaining products contained aberrant junctional sequences that may have been produced in a variation of the normal reaction. These results indicate that HIV IN protein is the only viral protein required to insert model HIV DNA sequences into a target DNA in vitro.

Guidelines for NASA Missions to Engage the User Community as a Part of the Mission Life Cycle

NASA Astrophysics Data System (ADS)

Escobar, V. M.; Friedl, L.; Bonniksen, C. K.

2017-12-01

NASA continues to improve the Earth Science Directorate in the areas of thematic integration, stakeholder feedback and Project Applications Program tailoring for missions to transfer knowledge between scientists and projects. The integration of application themes and the implementation of application science activities in flight projects have evolved to formally include user feedback and stakeholder integration. NASA's new Flight Applied Science Program Guidelines are designed to bridge NASA Earth Science Directorates in Flight, Applied Sciences and Research and Development by agreeing to integrate the user community into mission life cycles. Thus science development and science applications will guide all new instruments launched by NASAs ESD. The continued integration with the user community has enabled socio-economic considerations into NASA Earth Science projects to advance significantly. Making users a natural part of mission science leverages future socio-economic impact research and provides a platform for innovative and more actionable product to be used in decision support systems by society. This presentation will give an overview of the new NASA Guidelines and provide samples that demonstrate how the user community can be a part of NASA mission designs.

PDS MSL Analyst's Notebook: Supporting Active Rover Missions and Adding Value to Planetary Data Archives

NASA Astrophysics Data System (ADS)

Stein, Thomas

Planetary data archives of surface missions contain data from numerous hosted instruments. Because of the nondeterministic nature of surface missions, it is not possible to assess the data without understanding the context in which they were collected. The PDS Analyst’s Notebook (http://an.rsl.wustl.edu) provides access to Mars Science Laboratory (MSL) data archives by integrating sequence information, engineering and science data, observation planning and targeting, and documentation into web-accessible pages to facilitate “mission replay.” In addition, Mars Exploration Rover (MER), Mars Phoenix Lander, Lunar Apollo surface mission, and LCROSS mission data are available in the Analyst’s Notebook concept, and a Notebook is planned for the Insight mission. The MSL Analyst’s Notebook contains data, documentation, and support files for the Curiosity rovers. The inputs are incorporated on a daily basis into a science team version of the Notebook. The public version of the Analyst’s Notebook is comprised of peer-reviewed, released data and is updated coincident with PDS data releases as defined in mission archive plans. The data are provided by the instrument teams and are supported by documentation describing data format, content, and calibration. Both operations and science data products are included. The operations versions are generated to support mission planning and operations on a daily basis. They are geared toward researchers working on machine vision and engineering operations. Science versions of observations from some instruments are provided for those interested in radiometric and photometric analyses. Both data set documentation and sol (i.e., Mars day) documents are included in the Notebook. The sol documents are the mission manager and documentarian reports that provide a view into science operations—insight into why and how particular observations were made. Data set documents contain detailed information regarding the mission, spacecraft, instruments, and data formats. In addition, observation planning and targeting information is extracted from each sol’s tactical science plan. A number of methods allow user access to the Notebook contents. The mission summary provides a high level overview of science operations. The Sol Summaries are the primary interface to integrated data and documents contained within the Notebooks. Data, documents, and planned observations are grouped for easy scanning. Data products are displayed in order of acquisition, and are grouped into logical sequences, such as a series of image data. Sequences and the individual products that comprise them may be viewed in detail, manipulated, and downloaded. Color composites and anaglyph stereo images may be created on demand. Graphs of some non-image data, such as spectra, may be viewed. Data may be downloaded as zip or gzip files, or as multiband ENVI image files. The Notebook contains a map with the rover traverse plotted on a HiRISE basemap using the raw and corrected drive telemetry provided by the project. Users may zoom and pan the map. Clicking on a traverse location brings up links to corresponding data. Three types of searching through data and documents are available within the Notebook. Free text searching of data set and sol documents are supported. Data are searchable by instrument, acquisition time, data type, and product ID. Results may be downloaded in a single collection or selected individually for detailed viewing. Additional resources include data set documents, references to published mission, links to related web resources, and online help. Finally, feedback is handled through an online forum. Work continues to improve functionality, including locating features of interest and a spectral library search/view/download tool. A number of Notebook functions are based on previous user suggestions, and feedback continues to be sought. The Analyst’s Notebook is available at http://an.rsl.wustl.edu.

Critters: K-6 Life Science Activities. Project AIMS.

ERIC Educational Resources Information Center

Allen, Maureen Murphy; And Others

Project AIMS (Activities to Integrate Mathematics and Science) has as its purpose the integration of subject matter in grades K-9. Field testing of the curriculum materials produced by AIMS indicates that this integration produces the following beneficial results: (1) mathematics becomes more meaningful, hence more useful; (2) science is…

The Integration of Science and Mathematics Education: Highlights from the NSF/SSMA Wingspread Conference Plenary Papers.

ERIC Educational Resources Information Center

Berlin, Donna F.

1994-01-01

Summarizes plenary papers presented at the NSF/SSMA Wingspread Conference to explore ways to improve science and mathematics education through integration. Themes included analysis of integration; divergence of mathematics education from science education; technological perspectives; promoting mathematical and scientific inquiry; and school…

Science Integrating Learning Objectives: A Cooperative Learning Group Process

ERIC Educational Resources Information Center

Spindler, Matt

2015-01-01

The integration of agricultural and science curricular content that capitalizes on natural and inherent connections represents a challenge for secondary agricultural educators. The purpose of this case study was to create information about the employment of Cooperative Learning Groups (CLG) to enhance the science integrating learning objectives…

77 FR 21158 - VA Directive 0005 on Scientific Integrity: Availability for Review and Comment

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-09

... the Director, Office of Science and Technology Policy's Memorandum of December 17, 2010, on scientific integrity. It addresses how VA ensures quality science in its methods, review, policy application, and...: Background The Presidential Memorandum on Scientific Integrity and the Office of Science and Technology...

A question of style: method, integrity and the meaning of proper science.

PubMed

Penders, Bart; Vos, Rein; Horstman, Klasien

2009-09-01

Controversies in science often centre on methodology and integrity; these are the gatekeepers of proper science. But what exactly defines proper science as proper is not universal, especially in collaborative fields of enquiry where different perspectives meet. These encounters often result in friction, yet may equally give rise to new perspectives on proper science. A tour of collaborative endeavours like structural biology and nutrigenomics highlights some of those frictions and the controversies that can result from the encounter of 'wet' and 'dry' science. Attuning scientists to the plurality of proper science may safeguard many a scientist's integrity from being questioned unjustly.

The EBI search engine: EBI search as a service—making biological data accessible for all

PubMed Central

Park, Young M.; Squizzato, Silvano; Buso, Nicola; Gur, Tamer

2017-01-01

Abstract We present an update of the EBI Search engine, an easy-to-use fast text search and indexing system with powerful data navigation and retrieval capabilities. The interconnectivity that exists between data resources at EMBL–EBI provides easy, quick and precise navigation and a better understanding of the relationship between different data types that include nucleotide and protein sequences, genes, gene products, proteins, protein domains, protein families, enzymes and macromolecular structures, as well as the life science literature. EBI Search provides a powerful RESTful API that enables its integration into third-party portals, thus providing ‘Search as a Service’ capabilities, which are the main topic of this article. PMID:28472374

Comment on "Donders, T.H. 2014. Middle Holocene humidity increase in Florida: climate or sea-level? Quaternary Science Reviews 103:170-174."

USGS Publications Warehouse

Glaser, Paul H.; Hansen, Barbara CS; Donovan, Joseph J.; Givnish, Thomas J.; Stricker, Craig A.; Volin, John C.

2015-01-01

The NESRS site is located in an area where runoff collected from a 10,000 km2wetland prior to 1900 AD when most of the drainage from the Everglades was channeled to the sea through the narrow Shark River Slough. The sedimentary sequence at the NESRS site should therefore contain an integrated record of hydrological change across the pre-historical Everglades (Glaser et al., 2012). In addition this essentially non-forested wetland is well suited to accumulate a representative sample of the regional pollen rain in its sediments (e.g. Jaccobson and Bradshaw, 1981 and Prentice, 1985).

Parenting from before conception.

PubMed

Lane, Michelle; Robker, Rebecca L; Robertson, Sarah A

2014-08-15

At fertilization, the gametes endow the embryo with a genomic blueprint, the integrity of which is affected by the age and environmental exposures of both parents. Recent studies reveal that parental history and experiences also exert effects through epigenomic information not contained in the DNA sequence, including variations in sperm and oocyte cytosine methylation and chromatin patterning, noncoding RNAs, and mitochondria. Transgenerational epigenetic effects interact with conditions at conception to program the developmental trajectory of the embryo and fetus, ultimately affecting the lifetime health of the child. These insights compel us to revise generally held notions to accommodate the prospect that biological parenting commences well before birth, even prior to conception. Copyright © 2014, American Association for the Advancement of Science.

Terragenome: International Soil Metagenome Sequencing Consortium (GSC8 Meeting)

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

Jansson, Janet

2009-09-09

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Janet Jansson of the Lawrence Berkeley National Laboratory discusses the Terragenome Initiative at the Genomic Standards Consortium's 8th meeting at the DOE JGI inmore » Walnut Creek, CA on Sept. 9, 2009.« less

Sequencing the Unrearranged Human Immunoglobin

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

Warren, Rene

2010-06-03

Rene Warren from Canada's Michael Smith Genome Sciences Centre discusses sequencing and finishing the IgH heavy chain locus on June 3, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

Reduce costs with multimission sequencing and a multimission operations system

NASA Technical Reports Server (NTRS)

Bliss, D. A.; Morales, L. C.

2003-01-01

The paper will then propose extending this multi-mission philosophy to skeleton timeline development, science sequencing, and spacecraft sequencing. Finally, the paper will investigate a multi-mission approach to MOS development.

Integrated Science Assessments

EPA Pesticide Factsheets

Integrated Science Assessments are reports that represent a concise evaluation and synthesis of the most policy-relevant science for reviewing the National Ambient Air Quality Standards for the six principal pollutants.

Perspectives of teachers regarding the integration of mathematics and science at the secondary school level

NASA Astrophysics Data System (ADS)

Zolnierczyk, Joanna Asia

The integration of mathematics and science in secondary schools in the 21st century continues to be an important topic of practice and research. The purpose of my research study, which builds on studies by Frykholm and Glasson (2005) and Berlin and White (2010), is to explore the potential constraints and benefits of integrating mathematics and science in Ontario secondary schools based on the perspectives of in-service and pre-service teachers with various math and/or science backgrounds. A qualitative and quantitative research design with an exploratory approach was used. The qualitative data was collected from a sample of 12 in-service teachers with various math and/or science backgrounds recruited from two school boards in Eastern Ontario. The quantitative and some qualitative data was collected from a sample of 81 pre-service teachers from the Queen's University Bachelor of Education (B.Ed) program. Semi-structured interviews were conducted with the in-service teachers while a survey and a focus group was conducted with the pre-service teachers. Once the data was collected, the qualitative data were abductively analyzed. For the quantitative data, descriptive and inferential statistics (one-way ANOVAs and Pearson Chi Square analyses) were calculated to examine perspectives of teachers regardless of teaching background and to compare groups of teachers based on teaching background. The findings of this study suggest that in-service and pre-service teachers have a positive attitude towards the integration of math and science and view it as valuable to student learning and success. The pre-service teachers viewed the integration as easy and did not express concerns to this integration. On the other hand, the in-service teachers highlighted concerns and challenges such as resources, scheduling, and time constraints. My results illustrate when teachers perceive it is valuable to integrate math and science and which aspects of the classroom benefit best from the integration. Furthermore, the results highlight barriers and possible solutions to better the integration of math and science. In addition to the benefits and constraints of integration, my results illustrate why some teachers may opt out of integrating math and science and the different strategies teachers have incorporated to integrate math and science in their classroom.

Ozone (O3) Standards - Integrated Science Assessments from Review Completed in 2015

EPA Pesticide Factsheets

The integrated science assessment (ISA) is a comprehensive review, synthesis, and evaluation of the most policy-relevant science, including key science judgments that are important to inform the development of the risk and exposure assessments, and more.

Integrated sequencing of exome and mRNA of large-sized single cells.

PubMed

Wang, Lily Yan; Guo, Jiajie; Cao, Wei; Zhang, Meng; He, Jiankui; Li, Zhoufang

2018-01-10

Current approaches of single cell DNA-RNA integrated sequencing are difficult to call SNPs, because a large amount of DNA and RNA is lost during DNA-RNA separation. Here, we performed simultaneous single-cell exome and transcriptome sequencing on individual mouse oocytes. Using microinjection, we kept the nuclei intact to avoid DNA loss, while retaining the cytoplasm inside the cell membrane, to maximize the amount of DNA and RNA captured from the single cell. We then conducted exome-sequencing on the isolated nuclei and mRNA-sequencing on the enucleated cytoplasm. For single oocytes, exome-seq can cover up to 92% of exome region with an average sequencing depth of 10+, while mRNA-sequencing reveals more than 10,000 expressed genes in enucleated cytoplasm, with similar performance for intact oocytes. This approach provides unprecedented opportunities to study DNA-RNA regulation, such as RNA editing at single nucleotide level in oocytes. In future, this method can also be applied to other large cells, including neurons, large dendritic cells and large tumour cells for integrated exome and transcriptome sequencing.

Beyond integrating social sciences: Reflecting on the place of life sciences in empirical bioethics methodologies.

PubMed

Mertz, Marcel; Schildmann, Jan

2018-06-01

Empirical bioethics is commonly understood as integrating empirical research with normative-ethical research in order to address an ethical issue. Methodological analyses in empirical bioethics mainly focus on the integration of socio-empirical sciences (e.g. sociology or psychology) and normative ethics. But while there are numerous multidisciplinary research projects combining life sciences and normative ethics, there is few explicit methodological reflection on how to integrate both fields, or about the goals and rationales of such interdisciplinary cooperation. In this paper we will review some drivers for the tendency of empirical bioethics methodologies to focus on the collaboration of normative ethics with particularly social sciences. Subsequently, we argue that the ends of empirical bioethics, not the empirical methods, are decisive for the question of which empirical disciplines can contribute to empirical bioethics in a meaningful way. Using already existing types of research integration as a springboard, five possible types of research which encompass life sciences and normative analysis will illustrate how such cooperation can be conceptualized from a methodological perspective within empirical bioethics. We will conclude with a reflection on the limitations and challenges of empirical bioethics research that integrates life sciences.

Avatar DNA Nanohybrid System in Chip-on-a-Phone

NASA Astrophysics Data System (ADS)

Park, Dae-Hwan; Han, Chang Jo; Shul, Yong-Gun; Choy, Jin-Ho

2014-05-01

Long admired for informational role and recognition function in multidisciplinary science, DNA nanohybrids have been emerging as ideal materials for molecular nanotechnology and genetic information code. Here, we designed an optical machine-readable DNA icon on microarray, Avatar DNA, for automatic identification and data capture such as Quick Response and ColorZip codes. Avatar icon is made of telepathic DNA-DNA hybrids inscribed on chips, which can be identified by camera of smartphone with application software. Information encoded in base-sequences can be accessed by connecting an off-line icon to an on-line web-server network to provide message, index, or URL from database library. Avatar DNA is then converged with nano-bio-info-cogno science: each building block stands for inorganic nanosheets, nucleotides, digits, and pixels. This convergence could address item-level identification that strengthens supply-chain security for drug counterfeits. It can, therefore, provide molecular-level vision through mobile network to coordinate and integrate data management channels for visual detection and recording.

Avatar DNA Nanohybrid System in Chip-on-a-Phone

PubMed Central

Park, Dae-Hwan; Han, Chang Jo; Shul, Yong-Gun; Choy, Jin-Ho

2014-01-01

Long admired for informational role and recognition function in multidisciplinary science, DNA nanohybrids have been emerging as ideal materials for molecular nanotechnology and genetic information code. Here, we designed an optical machine-readable DNA icon on microarray, Avatar DNA, for automatic identification and data capture such as Quick Response and ColorZip codes. Avatar icon is made of telepathic DNA-DNA hybrids inscribed on chips, which can be identified by camera of smartphone with application software. Information encoded in base-sequences can be accessed by connecting an off-line icon to an on-line web-server network to provide message, index, or URL from database library. Avatar DNA is then converged with nano-bio-info-cogno science: each building block stands for inorganic nanosheets, nucleotides, digits, and pixels. This convergence could address item-level identification that strengthens supply-chain security for drug counterfeits. It can, therefore, provide molecular-level vision through mobile network to coordinate and integrate data management channels for visual detection and recording. PMID:24824876

Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration

PubMed Central

Miller, Thomas F.

2017-01-01

We present a coarse-grained simulation model that is capable of simulating the minute-timescale dynamics of protein translocation and membrane integration via the Sec translocon, while retaining sufficient chemical and structural detail to capture many of the sequence-specific interactions that drive these processes. The model includes accurate geometric representations of the ribosome and Sec translocon, obtained directly from experimental structures, and interactions parameterized from nearly 200 μs of residue-based coarse-grained molecular dynamics simulations. A protocol for mapping amino-acid sequences to coarse-grained beads enables the direct simulation of trajectories for the co-translational insertion of arbitrary polypeptide sequences into the Sec translocon. The model reproduces experimentally observed features of membrane protein integration, including the efficiency with which polypeptide domains integrate into the membrane, the variation in integration efficiency upon single amino-acid mutations, and the orientation of transmembrane domains. The central advantage of the model is that it connects sequence-level protein features to biological observables and timescales, enabling direct simulation for the mechanistic analysis of co-translational integration and for the engineering of membrane proteins with enhanced membrane integration efficiency. PMID:28328943

Preservice Mathematics and Science Teachers in an Integrated Teacher Preparation Program for Grades 7-12: A 3-Year Study of Attitudes and Perceptions Related to Integration

ERIC Educational Resources Information Center

Berlin, Donna F.; White, Arthur L.

2010-01-01

The purpose of this article is twofold: (a) to describe a unique teacher licensure program for grades 7-12 that integrates mathematics, science, and technology education and (b) to explore the attitudes and perceptions related to the integration of mathematics, science, and technology education of three cohorts of preservice teachers enrolled in…

Effectiveness of integrated science instructional material on pressure in daily life theme to improve digital age literacy of students

NASA Astrophysics Data System (ADS)

Asrizal; Amran, A.; Ananda, A.; Festiyed; Khairani, S.

2018-04-01

Integrated science learning and literacy skills are relevant issues in Indonesian’s education. However, the use of the integrated science learning and the integration of literacy in learning cannot be implemented well. An alternative solution of this problem is to develop integrated science instructional material on pressure in daily life theme by integrating digital age literacy. Purpose of research is to investigate the effectiveness of the use of integrated science instructional material on pressure in daily life theme to improve knowledge competence, attitudes competence and literacy skills of students. This research was a part of development research which has been conducted. In the product testing stage of this research and development was used before and after design of treatment for one sample group. Instruments to collect the data consist of learning outcomes test sheet, attitude observation sheet, and performance assessment sheet of students. Data analysis techniques include descriptive statistics analysis, normality test, homogeneity test, and paired comparison test. Therefore, the important result of research is the use of integrated science instructional material on pressure in daily life theme is effective in scientific approach to improve knowledge competence, attitudes competence, and digital age literacy skills of grade VIII students at 95% confidence level.

Technology Use in Science Instruction (TUSI): Aligning the Integration of Technology in Science Instruction in Ways Supportive of Science Education Reform

ERIC Educational Resources Information Center

Campbell, Todd; Abd-Hamid, Nor Hashidah

2013-01-01

This study describes the development of an instrument to investigate the extent to which technology is integrated in science instruction in ways aligned to science reform outlined in standards documents. The instrument was developed by: (a) creating items consistent with the five dimensions identified in science education literature, (b)…

Improving Student Science Literacy through an Inquiry-Based, Integrated Science Curriculum and Review of Science Media.

ERIC Educational Resources Information Center

Bardeen, Karen

This project studied the effects of an inquiry-based, integrated science course on student science literacy. The course was aligned to state and national science standards. The target population consisted of sophomore, junior, and senior high-school students in an upper-middle class suburb of a major Midwestern city. Questionnaires, tests, and…

Development of Contextual Mathematics teaching Material integrated related sciences and realistic for students grade xi senior high school

NASA Astrophysics Data System (ADS)

Helma, H.; Mirna, M.; Edizon, E.

2018-04-01

Mathematics is often applied in physics, chemistry, economics, engineering, and others. Besides that, mathematics is also used in everyday life. Learning mathematics in school should be associated with other sciences and everyday life. In this way, the learning of mathematics is more realstic, interesting, and meaningful. Needs analysis shows that required contextual mathematics teaching materials integrated related sciences and realistic on learning mathematics. The purpose of research is to produce a valid and practical contextual mathematics teaching material integrated related sciences and realistic. This research is development research. The result of this research is a valid and practical contextual mathematics teaching material integrated related sciences and realistic produced

Science IDEAS: A Research-Based K-5 Interdisciplinary Instructional Model Linking Science and Literacy

ERIC Educational Resources Information Center

Romance, Nancy R.; Vitale, Michael R.

2012-01-01

Science IDEAS is an evidence-based model that reflects interdisciplinary research findings that support the integration of literacy (e.g., reading comprehension) within science instruction in grades K-5. Presented is a framework for planning integrated science and literacy instruction in which six elements (hands-on investigations, reading,…

Kid's Eye View of Science: A Conceptual, Integrated Approach to Teaching Science, K-6

ERIC Educational Resources Information Center

Kovalik, Susan J.; Olsen, Karen D.

2010-01-01

This book examines learning science from multiple perspectives--especially a child's. The whimsical character of Mary Froggins guides readers through the steps of igniting students' natural sense of wonder, incorporating brain research, integrating science concepts with other subjects, and applying science to daily life. The authors demonstrate…

Relationships among Jamaican Ninth-Graders' Variables and Performance in Integrated Science

ERIC Educational Resources Information Center

Stockhausen, Novia; Soyibo, Kola

2004-01-01

This study assessed the level of integrated science performance of 200 Jamaican ninth-graders (100 boys, 100 girls), and determined if there were significant differences in their performance linked to their gender, attitudes to science, school location and student-type. A science achievement test and attitudes to science questionnaire were used…

Integrating the Nature of Science

ERIC Educational Resources Information Center

Weiland, Ingrid; Blieden, Katherine; Akerson, Valarie

2014-01-01

The nature of science (NOS) describes what science is and how knowledge in science is developed (NSTA 2013). To develop elementary students' understandings of how scientists explore the world, the authors--an education professor and a third-grade teacher--endeavored to integrate NOS into a third-grade life science unit. Throughout the lesson,…

Teacher Conceptions of Integrated STEM Education and How They Are Reflected in Integrated STEM Curriculum Writing and Classroom Implementation

NASA Astrophysics Data System (ADS)

Ring, Elizabeth A.

There has been a nation-wide push for an increase in the use of integrated science, technology, engineering, and mathematics (STEM) education in the United States. With this shift in epistemological, pedagogical, and curricular content, there is a need to develop an understanding as to what integrated STEM education is, particularly among practitioners. In this dissertation, inservice science teacher conceptions of integrated STEM education were investigated to help understand what these conceptions are and how these conceptions influence curriculum writing and implementation of integrated STEM curricula in classrooms. Teacher conceptions and their influences were investigated through three separate but interrelated studies. First, K-12 inservice science teachers' conceptions of integrated STEM were investigated through the analysis of their sketched models of integrated STEM education. How these models changed throughout an intensive, three-week professional development was also explored. The goal of this first study was to identify conceptual models of integrated STEM education held by inservice science teachers and to understand how these conceptions might change over the course of a professional development. Second, photo elicitation interviews (PEIs) and curricular analysis were used to provide rich descriptions of the conceptual models of integrated STEM education held by inservice science teachers, determine what components of STEM inservice science teachers found fundamental to integrating STEM in the classroom based on their conceptions, and explore how teachers' conceptions of STEM were used in their development of integrated STEM curricula. The goal of this second study was to better understand inservice science teachers' conceptual models of integrated STEM and explore how these models were realized in the teachers' curriculum writing. Third, a multiple-case study was conducted with three teachers to investigate how the conceptual models held by inservice science teachers were enacted in their implementation of an integrated STEM curriculum unit in their classrooms. The goal of this third study was to determine how, if at all, teachers enact their conceptual models of integrated STEM education in the classroom when implementing a STEM curriculum. Together, these three studies helped to broaden the research related to integrated STEM education in the literature. The progressive nature of the studies in this dissertation, as well as the diverse use of methodologies and data analysis, helped to expand STEM education research.

Tech-Savvy Science Education? Understanding Teacher Pedagogical Practices for Integrating Technology in K-12 Classrooms

ERIC Educational Resources Information Center

Hechter, Richard; Vermette, Laurie Anne

2014-01-01

This paper examines the technology integration practices of Manitoban K-12 inservice science educators based on the Technological, Pedagogical, and Content knowledge (TPACK) framework. Science teachers (n = 433) completed a 10-item online survey regarding pedagogical beliefs about technology integration, types of technology used, and how often…

Preparing Middle Level Preservice Teachers to Integrate Mathematics and Science: Problems and Possibilities

ERIC Educational Resources Information Center

Koirala, Hari P.; Bowman, Jacqueline K.

2003-01-01

Many members of the mathematics and science education community believe that the integration of mathematics and science enhances students' understanding of both subjects. Despite this belief, attempts to integrate these subjects have frequently been unsuccessful. This study examines the development and implementation of a team-taught integrated…

From PCK to TPACK: Developing a Transformative Model for Pre-Service Science Teachers

ERIC Educational Resources Information Center

Jang, Syh-Jong; Chen, Kuan-Chung

2010-01-01

New science teachers should be equipped with the ability to integrate and design the curriculum and technology for innovative teaching. How to integrate technology into pre-service science teachers' pedagogical content knowledge is the important issue. This study examined the impact on a transformative model of integrating technology and peer…

Detection of integrated papillomavirus sequences by ligation-mediated PCR (DIPS-PCR) and molecular characterization in cervical cancer cells.

PubMed

Luft, F; Klaes, R; Nees, M; Dürst, M; Heilmann, V; Melsheimer, P; von Knebel Doeberitz, M

2001-04-01

Human papillomavirus (HPV) genomes usually persist as episomal molecules in HPV associated preneoplastic lesions whereas they are frequently integrated into the host cell genome in HPV-related cancers cells. This suggests that malignant conversion of HPV-infected epithelia is linked to recombination of cellular and viral sequences. Due to technical limitations, precise sequence information on viral-cellular junctions were obtained only for few cell lines and primary lesions. In order to facilitate the molecular analysis of genomic HPV integration, we established a ligation-mediated PCR assay for the detection of integrated papillomavirus sequences (DIPS-PCR). DIPS-PCR was initially used to amplify genomic viral-cellular junctions from HPV-associated cervical cancer cell lines (C4-I, C4-II, SW756, and HeLa) and HPV-immortalized keratinocyte lines (HPKIA, HPKII). In addition to junctions already reported in public data bases, various new fusion fragments were identified. Subsequently, 22 different viral-cellular junctions were amplified from 17 cervical carcinomas and 1 vulval intraepithelial neoplasia (VIN III). Sequence analysis of each junction revealed that the viral E1 open reading frame (ORF) was fused to cellular sequences in 20 of 22 (91%) cases. Chromosomal integration loci mapped to chromosomes 1 (2n), 2 (3n), 7 (2n), 8 (3n), 10 (1n), 14 (5n), 16 (1n), 17 (2n), and mitochondrial DNA (1n), suggesting random distribution of chromosomal integration sites. Precise sequence information obtained by DIPS-PCR was further used to monitor the monoclonal origin of 4 cervical cancers, 1 case of recurrent premalignant lesions and 1 lymph node metastasis. Therefore, DIPS-PCR might allow efficient therapy control and prediction of relapse in patients with HPV-associated anogenital cancers. Copyright 2001 Wiley-Liss, Inc.

Distinct patterns of alteration of myc genes associated with integration of human papillomavirus type 16 or type 45 DNA in two genital tumours.

PubMed

Sastre-Garau, X; Favre, M; Couturier, J; Orth, G

2000-08-01

We previously described two genital carcinomas (IC2, IC4) containing human papillomavirus type 16 (HPV-16)- or HPV-18-related sequences integrated in chromosomal bands containing the c-myc (8q24) or N-myc (2p24) gene, respectively. The c-myc gene was rearranged and amplified in IC2 cells without evidence of overexpression. The N-myc gene was amplified and highly transcribed in IC4 cells. Here, the sequence of an 8039 bp IC4 DNA fragment containing the integrated viral sequences and the cellular junctions is reported. A 3948 bp segment of the genome of HPV-45 encompassing the upstream regulatory region and the E6 and E7 ORFs was integrated into the untranslated part of N-myc exon 3, upstream of the N-myc polyadenylation signal. Both N-myc and HPV-45 sequences were amplified 10- to 20-fold. The 3' ends of the major N-myc transcript were mapped upstream of the 5' junction. A minor N-myc/HPV-45 fusion transcript was also identified, as well as two abundant transcripts from the HPV-45 E6-E7 region. Large amounts of N-myc protein were detected in IC4 cells. A major alteration of c-myc sequences in IC2 cells involved the insertion of a non-coding sequence into the second intron and their co-amplification with the third exon, without any evidence for the integration of HPV-16 sequences within or close to the gene. Different patterns of myc gene alterations may thus be associated with integration of HPV DNA in genital tumours, including the activation of the protooncogene via a mechanism of insertional mutagenesis and/or gene amplification.

The role of university research in primary and secondary education

NASA Astrophysics Data System (ADS)

Redondo, A.; Llopart, M.; Ramos, L.; Roger, T.; Rafols, R.; Redondo, J. M.

2009-04-01

One of the most important roles of educators at all levels(transversally and inter-generationally between adult education, university and the primary schools, specially in sciences is to estimulate the quest for new knowledge and to help to provide the basic thinking tools of the proper scientific method. An innovative plan has been set up though the Campus Universitari de la Mediterrania that integrates the UPC, the local Education authorities and the local governement in Vilanova i la Geltru, Barcelona. To coordinate university professors invited to lecture in summer courses, so their research and lecturing materials may be used as school level material (as a CD collection) and to help younger students to iniciate their own research proyects. During 2006-2008 a series of Environmental science seminars, group proyects decided by the students or proposed jointly by the CUM were started. Examples of these works, such as Cetacean comunication (with the help of the Laboratory of Bioacustic Applications of the UPC), Shapes and patterns in the environment (Cosmocaixa Science Museum), the Rainbow, Waves and Tides, Turbulence, The growth of snails and the Fibonacci sequence, etc... will be presented, showing the importance of comunicating scientific interest to the younger generations.

Life sciences flight experiments program, life sciences project division, procurement quality provisions

NASA Technical Reports Server (NTRS)

House, G.

1980-01-01

Methods are defined for implementing quality assurance policy and requirements for life sciences laboratory equipment, experimental hardware, integration and test support equipment, and integrated payloads.

ECHOS: Early Childhood Hands-On Science Efficacy Study

ERIC Educational Resources Information Center

Brown, Judy A.; Greenfield, Daryl B.; Bell, Elizabeth; Juárez, Cheryl Lani; Myers, Ted; Nayfeld, Irena

2013-01-01

"ECHOS: Early Childhood Hands-On Science" was developed at the Miami Science Museum as a comprehensive set of science lessons sequenced to lead children toward a deeper understanding of science content and the use of science process skills. The purpose of the research is to determine whether use of the "ECHOS" model will…

Hybrid genome assembly and annotation of Paenibacillus pasadenensis strain R16 reveals insights on endophytic life style and antifungal activity

PubMed Central

Passera, Alessandro; Marcolungo, Luca; Brasca, Milena; Quaglino, Fabio; Cantaloni, Chiara; Delledonne, Massimo

2018-01-01

Bacteria of the Paenibacillus genus are becoming important in many fields of science, including agriculture, for their positive effects on the health of plants. However, there are little information available on this genus compared to other bacteria (such as Bacillus or Pseudomonas), especially when considering genomic information. Sequencing the genomes of plant-beneficial bacteria is a crucial step to identify the genetic elements underlying the adaptation to life inside a plant host and, in particular, which of these features determine the differences between a helpful microorganism and a pathogenic one. In this study, we have characterized the genome of Paenibacillus pasadenensis, strain R16, recently investigated for its antifungal activities and plant-associated features. An hybrid assembly approach was used integrating the very precise reads obtained by Illumina technology and long fragments acquired with Oxford Nanopore Technology (ONT) sequencing. De novo genome assembly based solely on Illumina reads generated a relatively fragmented assembly of 5.72 Mbp in 99 ungapped sequences with an N50 length of 544 Kbp; hybrid assembly, integrating Illumina and ONT reads, improved the assembly quality, generating a genome of 5.75 Mbp, organized in 6 contigs with an N50 length of 3.4 Mbp. Annotation of the latter genome identified 4987 coding sequences, of which 1610 are hypothetical proteins. Enrichment analysis identified pathways of particular interest for the endophyte biology, including the chitin-utilization pathway and the incomplete siderophore pathway which hints at siderophore parasitism. In addition the analysis led to the identification of genes for the production of terpenes, as for example farnesol, that was hypothesized as the main antifungal molecule produced by the strain. The functional analysis on the genome confirmed several plant-associated, plant-growth promotion, and biocontrol traits of strain R16, thus adding insights in the genetic bases of these complex features, and of the Paenibacillus genus in general. PMID:29351296

DNA sequencing using polymerase substrate-binding kinetics

PubMed Central

Previte, Michael John Robert; Zhou, Chunhong; Kellinger, Matthew; Pantoja, Rigo; Chen, Cheng-Yao; Shi, Jin; Wang, BeiBei; Kia, Amirali; Etchin, Sergey; Vieceli, John; Nikoomanzar, Ali; Bomati, Erin; Gloeckner, Christian; Ronaghi, Mostafa; He, Molly Min

2015-01-01

Next-generation sequencing (NGS) has transformed genomic research by decreasing the cost of sequencing. However, whole-genome sequencing is still costly and complex for diagnostics purposes. In the clinical space, targeted sequencing has the advantage of allowing researchers to focus on specific genes of interest. Routine clinical use of targeted NGS mandates inexpensive instruments, fast turnaround time and an integrated and robust workflow. Here we demonstrate a version of the Sequencing by Synthesis (SBS) chemistry that potentially can become a preferred targeted sequencing method in the clinical space. This sequencing chemistry uses natural nucleotides and is based on real-time recording of the differential polymerase/DNA-binding kinetics in the presence of correct or mismatch nucleotides. This ensemble SBS chemistry has been implemented on an existing Illumina sequencing platform with integrated cluster amplification. We discuss the advantages of this sequencing chemistry for targeted sequencing as well as its limitations for other applications. PMID:25612848

The Monsoon-90 / SALSA / EOS / SUDMED / SAHRA / HELP / USPP Experience: A Progression of Interdisciplinary Integration of Science and Decision Making over 20 years.

NASA Astrophysics Data System (ADS)

Chehbouni, G.; Goodrich, D.; Kustas, B.; Sorooshian, S.; Shuttleworth, J.; Richter, H.

2008-12-01

The Monsoon'90 Experiment conducted at the USDA-ARS Walnut Gulch Experimental Watershed in southeast Arizona was the start of a long arc of subsequent experiments and research that were larger, longer-term, more international, more interdisciplinary, and led to more direct integration of science for decision making and watershed management. In this era, much of our research and science must be more directly relevant to decision-makers and natural resource managers as they increasingly require sophisticated levels of expert findings and scientific results (e.g. interdisciplinary) to make informed decisions. Significant effort beyond focused, single disciplinary research is required conduct interdisciplinary science typical in large scale field experiments. Even greater effort is required to effectively integrate our research across the physical and ecological sciences for direct use by policy and decision makers. This presentation will provide an overview of the evolution of this arc of experiments and long-term projects into a mature integrated science and decision making program. It will discuss the transition in project focus from science and research for understanding; through science for addressing a need; to integrated science and policy development. At each stage the research conducted became more interdisciplinary, first across abiotic disciplines (hydrology, remote sensing, atmospheric science), then by merging abiotic and biotic disciplines (adding ecology and plant physiology), and finally a further integration of economic and social sciences with and policy and decision making for resource management. Lessons learned from this experience will be reviewed with the intent providing guidance to ensure that the resulting research is socially and scientifically relevant and will not only result in cutting edge science but will also directly address the needs of policy makers and resource managers.

Linking Science and Language Arts: A Review of the Literature Which Compares Integrated Versus Non-integrated Approaches

NASA Astrophysics Data System (ADS)

Bradbury, Leslie U.

2014-06-01

The purpose of this paper is to review the literature published during the last 20 years that investigates the impact of approaches that describe themselves as integrating science and language arts on student learning and/or attitude at the elementary level. The majority of papers report that integrated approaches led to greater student achievement in science and language arts across elementary grade levels. Additionally, integrated approaches facilitate improved attitudes toward both science and reading. The second section of the findings provides an overview of the types of pedagogical approaches used in the classrooms described in the studies. At all grade levels, teachers linked a variety of strategies including read-alouds, independent reading, at home reading, and writing in various genres that connected hands-on science activities to language arts skills.

Common Viral Integration Sites Identified in Avian Leukosis Virus-Induced B-Cell Lymphomas

PubMed Central

Justice, James F.; Morgan, Robin W.

2015-01-01

ABSTRACT Avian leukosis virus (ALV) induces B-cell lymphoma and other neoplasms in chickens by integrating within or near cancer genes and perturbing their expression. Four genes—MYC, MYB, Mir-155, and TERT—have previously been identified as common integration sites in these virus-induced lymphomas and are thought to play a causal role in tumorigenesis. In this study, we employ high-throughput sequencing to identify additional genes driving tumorigenesis in ALV-induced B-cell lymphomas. In addition to the four genes implicated previously, we identify other genes as common integration sites, including TNFRSF1A, MEF2C, CTDSPL, TAB2, RUNX1, MLL5, CXorf57, and BACH2. We also analyze the genome-wide ALV integration landscape in vivo and find increased frequency of ALV integration near transcriptional start sites and within transcripts. Previous work has shown ALV prefers a weak consensus sequence for integration in cultured human cells. We confirm this consensus sequence for ALV integration in vivo in the chicken genome. PMID:26670384

Advances in the NASA Earth Science Division Applied Science Program

NASA Astrophysics Data System (ADS)

Friedl, L.; Bonniksen, C. K.; Escobar, V. M.

2016-12-01

The NASA Earth Science Division's Applied Science Program advances the understanding of and ability to used remote sensing data in support of socio-economic needs. The integration of socio-economic considerations in to NASA Earth Science projects has advanced significantly. The large variety of acquisition methods used has required innovative implementation options. The integration of application themes and the implementation of application science activities in flight project is continuing to evolve. The creation of the recently released Earth Science Division, Directive on Project Applications Program and the addition of an application science requirement in the recent EVM-2 solicitation document NASA's current intent. Continuing improvement in the Earth Science Applications Science Program are expected in the areas of thematic integration, Project Applications Program tailoring for Class D missions and transfer of knowledge between scientists and projects.

Exploring relationships between the use of affect in science instruction and the pressures of a high-stakes testing environment

NASA Astrophysics Data System (ADS)

Jerome, Diane C.

This study explored how science teachers and school administrators perceive the use of the affective domain during science instruction situated within a high-stakes testing environment. Through a multimethodological inquiry using phenomenology and critical ethnography, the researcher conducted semi-structured interviews with six fifth-grade science teachers and two administrators from two Texas school districts. Data reconstructions from interviews formed a bricolage of diagrams that trace the researcher's steps through a reflective exploration of these phenomena. This study addressed the following research questions: (a) What are the attitudes, interests, and values (affective domain) that fifth-grade science teachers integrate into science instruction? (b) How do fifth-grade science teachers attempt to integrate attitudes, interests and values (affective domain) in science instruction? and (c) How do fifth-grade science teachers manage to balance the tension from the seeming pressures caused by a high-stakes testing environment and the integration of attitudes, interests and values (affective domain) in science instruction? The findings from this study indicate that as teachers tried to integrate the affective domain during science instruction, (a) their work was set within a framework of institutional values, (b) teaching science for understanding looked different before and after the onset of the science Texas Assessment of Knowledge and Skills (TAKS), and (c) upon administration of the science TAKS---teachers broadened their aim, raised their expectations, and furthered their professional development. The integration of the affective domain fell into two distinct categories: 1) teachers targeted student affect and 2) teachers modeled affective behavior.

Envisioning a Future of Computational Geoscience in a Data Rich Semantic World

NASA Astrophysics Data System (ADS)

Kumar, P.; Elag, M.; Jiang, P.; Marini, L.

2015-12-01

Advances in observational systems and reduction in their cost are allowing us to explore, monitor, and digitally represent our environment in unprecedented details and over large areas. Low cost in situ sensors, unmanned autonomous vehicles, imaging technologies, and other new observational approaches along with airborne and space borne systems are allowing us to measure nearly everything, almost everywhere, and at almost all the time. Under the aegis of observatories they are enabling an integrated view across space and time scales ranging from storms to seasons to years and, in some cases, decades. Rapid increase in the convergence of computational, communication and information systems and their inter-operability through advances in technologies such as semantic web can provide opportunities to further facilitate fusion and synthesis of heterogeneous measurements with knowledge systems. This integration can enable us to break disciplinary boundaries and bring sensor data directly to desktop or handheld devices. We describe CyberInfrastructure effort that is being developed through projects such as Earthcube Geosemantics (http://geosemantics.hydrocomplexity.net), (SEAD (http://sead-data.net/), and Browndog (http://browndog.ncsa.illinois.edu/)s o that data across all of earth science can be easily shared and integrated with models. This also includes efforts to enable models to become interoperable among themselves and with data using technologies that enable human-out-of-the-loop integration. Through such technologies our ability to use real time information for decision-making and scientific investigations will increase multifold. The data goes through a sequence of steps, often iterative, from collection to long-term preservation. Similarly the scientific investigation and associated outcomes are composed of a number of iterative steps from problem identification to solutions. However, the integration between these two pathways is rather limited. We describe characteristics of new technologies that are needed to bring these processes together in the near future to significantly reduce the latency between data, science, and agile and informed actions that support sustainability.

The emerging genomics and systems biology research lead to systems genomics studies.

PubMed

Yang, Mary Qu; Yoshigoe, Kenji; Yang, William; Tong, Weida; Qin, Xiang; Dunker, A; Chen, Zhongxue; Arbania, Hamid R; Liu, Jun S; Niemierko, Andrzej; Yang, Jack Y

2014-01-01

Synergistically integrating multi-layer genomic data at systems level not only can lead to deeper insights into the molecular mechanisms related to disease initiation and progression, but also can guide pathway-based biomarker and drug target identification. With the advent of high-throughput next-generation sequencing technologies, sequencing both DNA and RNA has generated multi-layer genomic data that can provide DNA polymorphism, non-coding RNA, messenger RNA, gene expression, isoform and alternative splicing information. Systems biology on the other hand studies complex biological systems, particularly systematic study of complex molecular interactions within specific cells or organisms. Genomics and molecular systems biology can be merged into the study of genomic profiles and implicated biological functions at cellular or organism level. The prospectively emerging field can be referred to as systems genomics or genomic systems biology. The Mid-South Bioinformatics Centre (MBC) and Joint Bioinformatics Ph.D. Program of University of Arkansas at Little Rock and University of Arkansas for Medical Sciences are particularly interested in promoting education and research advancement in this prospectively emerging field. Based on past investigations and research outcomes, MBC is further utilizing differential gene and isoform/exon expression from RNA-seq and co-regulation from the ChiP-seq specific for different phenotypes in combination with protein-protein interactions, and protein-DNA interactions to construct high-level gene networks for an integrative genome-phoneme investigation at systems biology level.

Goodbye genome paper, hello genome report: the increasing popularity of 'genome announcements' and their impact on science.

PubMed

Smith, David Roy

2017-05-01

Next-generation sequencing technologies have revolutionized genomics and altered the scientific publication landscape. Life-science journals abound with genome papers-peer-reviewed descriptions of newly sequenced chromosomes. Although they once filled the pages of Nature and Science, genome papers are now mostly relegated to journals with low-impact factors. Some have forecast the death of the genome paper and argued that they are using up valuable resources and not advancing science. However, the publication rate of genome papers is on the rise. This increase is largely because some journals have created a new category of manuscript called genome reports, which are short, fast-tracked papers describing a chromosome sequence(s), its GenBank accession number and little else. In 2015, for example, more than 2000 genome reports were published, and 2016 is poised to bring even more. Here, I highlight the growing popularity of genome reports and discuss their merits, drawbacks and impact on science and the academic publication infrastructure. Genome reports can be excellent assets for the research community, but they are also being used as quick and easy routes to a publication, and in some instances they are not peer reviewed. One of the best arguments for genome reports is that they are a citable, user-generated genomic resource providing essential methodological and biological information, which may not be present in the sequence database. But they are expensive and time-consuming avenues for achieving such a goal. © The Author 2016. Published by Oxford University Press.

Science Education: From Separation to Integration

ERIC Educational Resources Information Center

Linn, Marcia C.; Gerard, Libby; Matuk, Camillia; McElhaney, Kevin W.

2016-01-01

Advances in technology, science, and learning sciences research over the past 100 years have reshaped science education. This chapter focuses on how investigators from varied fields of inquiry who initially worked separately began to interact, eventually formed partnerships, and recently integrated their perspectives to strengthen science…

A Randomized Study of a Literacy-Integrated Science Intervention for Low-Socio-economic Status Middle School Students: Findings from first-year implementation

NASA Astrophysics Data System (ADS)

Tong, Fuhui; Irby, Beverly J.; Lara-Alecio, Rafael; Guerrero, Cindy; Fan, Yinan; Huerta, Margarita

2014-08-01

This paper presents the findings from a randomized control trial study of reading/literacy-integrated science inquiry intervention after 1 year of implementation and the treatment effect on 5th-grade low-socio-economic African-American and Hispanic students' achievement in science and English reading. A total of 94 treatment students and 194 comparison students from four randomized intermediate schools participated in the current project. The intervention consisted of ongoing professional development and specific instructional science lessons with inquiry-based learning, direct and explicit vocabulary instruction, and integration of reading and writing. Results suggested that (a) there was a significantly positive treatment effect as reflected in students' higher performance in district-wide curriculum-based tests of science and reading and standardized tests of science, reading, and English reading fluency; (b) males and females did not differ significantly from participating in science inquiry instruction; (c) African-American students had lower chance of sufficiently mastering the science concepts and achieving above the state standards when compared with Hispanic students across gender and condition, and (d) below-poverty African-American females are the most vulnerable group in science learning. Our study confirmed that even a modest amount of literacy integration in inquiry-based science instruction can promote students' science and reading achievement. Therefore, we call for more experimental research that focus on the quality of literacy-integrated science instruction from which middle grade students, particularly low-socio-economic status students, can benefit.

Integrating Forensic Science.

ERIC Educational Resources Information Center

Funkhouser, John; Deslich, Barbara J.

2000-01-01

Explains the implementation of forensic science in an integrated curriculum and discusses the advantages of this approach. Lists the forensic science course syllabi studied in three high schools. Discusses the unit on polymers in detail. (YDS)

Learning for Everyday Life: Students' standpoints on loud sounds and use of hearing protectors before and after a teaching-learning intervention

NASA Astrophysics Data System (ADS)

West, Eva

2012-11-01

Researchers have highlighted the increasing problem of loud sounds among young people in leisure-time environments, recently even emphasizing portable music players, because of the risk of suffering from hearing impairments such as tinnitus. However, there is a lack of studies investigating compulsory-school students' standpoints and explanations in connection with teaching interventions integrating school subject content with auditory health. In addition, there are few health-related studies in the international science education literature. This paper explores students' standpoints on loud sounds including the use of hearing-protection devices in connection with a teaching intervention based on a teaching-learning sequence about sound, hearing and auditory health. Questionnaire data from 199 students, in grades 4, 7 and 8 (aged 10-14), from pre-, post- and delayed post-tests were analysed. Additionally, information on their experiences of tinnitus as well as their listening habits regarding portable music players was collected. The results show that more students make healthier choices in questions of loud sounds after the intervention, and especially among the older ones this result remains or is further improved one year later. There are also signs of positive behavioural change in relation to loud sounds. Significant gender differences are found; generally, the girls show more healthy standpoints and expressions than boys do. If this can be considered to be an outcome of students' improved and integrated knowledge about sound, hearing and health, then this emphasizes the importance of integrating health issues into regular school science.

The Interplay of Representations and Patterns of Classroom Discourse in Science Teaching Sequences

ERIC Educational Resources Information Center

Tang, Kok-Sing

2016-01-01

The purpose of this study is to examines the relationship between the communicative approach of classroom talk and the modes of representations used by science teachers. Based on video data from two physics classrooms in Singapore, a recurring pattern in the relationship was observed as the teaching sequence of a lesson unfolded. It was found that…

A Teaching-Learning Sequence of Colour Informed by History and Philosophy of Science

ERIC Educational Resources Information Center

Maurício, Paulo; Valente, Bianor; Chagas, Isabel

2017-01-01

In this work, we present a teaching-learning sequence on colour intended to a pre-service elementary teacher programme informed by History and Philosophy of Science. Working in a socio-constructivist framework, we made an excursion on the history of colour. Our excursion through history of colour, as well as the reported misconception on colour…

What Difference Does Art Make in Science? A Comparative Study of Meaning-Making at Elementary School

ERIC Educational Resources Information Center

Jakobson, Britt; Wickman, Per-Olof

2015-01-01

Here we examine the role art activities play in aesthetic experience and learning of science. We compare recordings of two sequential occurrences in an elementary school class. The purpose of the first sequence was scientific and involved the children in observing leaves with magnifiers. The second sequence had an artistic purpose, where the…

Applications and Case Studies of the Next-Generation Sequencing Technologies in Food, Nutrition and Agriculture.

USDA-ARS?s Scientific Manuscript database

Next-generation sequencing technologies are able to produce high-throughput short sequence reads in a cost-effective fashion. The emergence of these technologies has not only facilitated genome sequencing but also changed the landscape of life sciences. Here I survey their major applications ranging...

Recent Applications of DNA Sequencing Technologies in Food, Nutrition and Agriculture

USDA-ARS?s Scientific Manuscript database

Next-generation DNA sequencing technologies are able to produce millions of short sequence reads in a high-throughput, cost-effective fashion. The emergence of these technologies has not only facilitated genome sequencing but also changed the landscape of life sciences. This review surveys their rec...

Next generation sequencers: methods and applications in food-borne pathogens

USDA-ARS?s Scientific Manuscript database

Next generation sequencers are able to produce millions of short sequence reads in a high-throughput, low-cost way. The emergence of these technologies has not only facilitated genome sequencing but also started to change the landscape of life sciences. This chapter will survey their methods and app...

Anticipating Change: An Exploratory Analysis of Teachers' Conceptions of Engineering in an Era of Science Education Reform

ERIC Educational Resources Information Center

Sengupta-Irving, Tesha; Mercado, Janet

2017-01-01

While integrating engineering into science education is not new in the United States, technology and engineering have not been well emphasized in the preparation and professional development of science teachers. Recent science education reforms integrate science and engineering throughout K-12 education, making it imperative to explore the…

The Impact of Engineering Integrated Science (EIS) Curricula on First-Year Technical High School Students' Attitudes toward Science and Perceptions of Engineering

ERIC Educational Resources Information Center

Nam, Younkyeong; Lee, Sun-Ju; Paik, Seoung-Hey

2016-01-01

This study investigated how engineering integrated science (EIS) curricula affect first-year technical high school students' attitudes toward science and perceptions of engineering. The effect of the EIS participation period on students' attitudes toward science was also investigated via experimental study design. Two engineering integrated…

Authentic Integration: a model for integrating mathematics and science in the classroom

NASA Astrophysics Data System (ADS)

Treacy, Páraic; O'Donoghue, John

2014-07-01

Attempts at integrating mathematics and science have been made previously but no definitive, widely adopted teaching model has been developed to date. Research suggests that hands-on, practical, student-centred tasks should form a central element when designing an effective model for the integration of mathematics and science. Aided by this research, the author created a new model entitled 'Authentic Integration' which caters for the specific needs of integration of mathematics and science. This model requires that each lesson be based around a rich task which relates to the real world and ensures that hands-on group work, inquiry, and discussion are central to the lesson. It was found that Authentic Integration, when applied in four Irish post-primary schools, positively affected pupil understanding. The teachers who completed the intervention displayed a very positive attitude towards the approach, intimating that they would continue to implement the practice in their classrooms.

Patterns of Viral DNA Integration in Cells Transformed by Wild Type or DNA-Binding Protein Mutants of Adenovirus Type 5 and Effect of Chemical Carcinogens on Integration

PubMed Central

Dorsch-Häsler, Karoline; Fisher, Paul B.; Weinstein, I. Bernard; Ginsberg, Harold S.

1980-01-01

The integration pattern of viral DNA was studied in a number of cell lines transformed by wild-type adenovirus type 5 (Ad5 WT) and two mutants of the DNA-binding protein gene, H5ts125 and H5ts107. The effect of chemical carcinogens on the integration of viral DNA was also investigated. Liquid hybridization (C0t) analyses showed that rat embryo cells transformed by Ad5 WT usually contained only the left-hand end of the viral genome, whereas cell lines transformed by H5ts125 or H5ts107 at either the semipermissive (36°C) or nonpermissive (39.5°C) temperature often contained one to five copies of all or most of the entire adenovirus genome. The arrangement of the integrated adenovirus DNA sequences was determined by cleavage of transformed cell DNA with restriction endonucleases XbaI, EcoRI, or HindIII followed by transfer of separated fragments to nitrocellulose paper and hybridization according to the technique of E. M. Southern (J. Mol. Biol. 98: 503-517, 1975). It was found that the adenovirus genome is integrated as a linear sequence covalently linked to host cell DNA; that the viral DNA is integrated into different host DNA sequences in each cell line studied; that in cell lines that contain multiple copies of the Ad5 genome the viral DNA sequences can be integrated in a single set of host cell DNA sequences and not as concatemers; and that chemical carcinogens do not alter the extent or pattern of viral DNA integration. Images PMID:6246266

A Cooperative Learning Group Procedure for Improving CTE and Science Integration

ERIC Educational Resources Information Center

Spindler, Matt

2016-01-01

The purpose of this case study was to create information about the employment of Cooperative Learning Groups (CLG) to enhance the science integrating learning objectives utilized in secondary CTE courses. The objectives of the study were to determine if CLGs were an effective means for increasing the number of: a) science integrating learning…

Traditional Ecological Knowledge in Science Education and Its Integration in Grades 7 and 8 Canadian Science Curriculum Documents

ERIC Educational Resources Information Center

Kim, Eun-Ji Amy; Dionne, Liliane

2014-01-01

Though science education has been prominent in the Canadian educational system, researchers increasingly recognize the scientific and educational value of integrating traditional ecological knowledge (TEK) into their curriculum. Despite national strategies to integrate TEK, Canada has yet to initiate a comprehensive study of its prevalence and…

Math, Science, and Engineering Integration in a High School Engineering Course: A Qualitative Study

ERIC Educational Resources Information Center

Valtorta, Clara G.; Berland, Leema K.

2015-01-01

Engineering in K-12 classrooms has been receiving expanding emphasis in the United States. The integration of science, mathematics, and engineering is a benefit and goal of K-12 engineering; however, current empirical research on the efficacy of K-12 science, mathematics, and engineering integration is limited. This study adds to this growing…

Exploration of Secondary Students' Creativity by Integrating Web-Based Technology into an Innovative Science Curriculum

ERIC Educational Resources Information Center

Jang, Syh-Jong

2009-01-01

The purpose of the study was to investigate how web-based technology could be utilized and integrated with real-life scientific materials to stimulate the creativity of secondary school students. One certified science teacher and 31 seventh graders participated in this study. Several real-life experience science sessions integrated with online…

Dawn Mission Education and Public Outreach: Science as Human Endeavor

NASA Astrophysics Data System (ADS)

Cobb, W. H.; Wise, J.; Schmidt, B. E.; Ristvey, J.

2012-12-01

Dawn Education and Public Outreach strives to reach diverse learners using multi-disciplinary approaches. In-depth professional development workshops in collaboration with NASA's Discovery Program, MESSENGER and Stardust-NExT missions focusing on STEM initiatives that integrate the arts have met the needs of diverse audiences and received excellent evaluations. Another collaboration on NASA ROSES grant, Small Bodies, Big Concepts, has helped bridge the learning sequence between the upper elementary and middle school, and the middle and high school Dawn curriculum modules. Leveraging the Small Bodies, Big Concepts model, educators experience diverse and developmentally appropriate NASA activities that tell the Dawn story, with teachers' pedagogical skills enriched by strategies drawn from NSTA's Designing Effective Science Instruction. Dawn mission members enrich workshops by offering science presentations to highlight events and emerging data. Teachers' awareness of the process of learning new content is heightened, and they use that experience to deepen their science teaching practice. Activities are sequenced to enhance conceptual understanding of big ideas in space science and Vesta and Ceres and the Dawn Mission 's place within that body of knowledge Other media add depth to Dawn's resources for reaching students. Instrument and ion engine interactives developed with the respective science team leads help audiences engage with the mission payload and the data each instrument collects. The Dawn Dictionary, an offering in both audio as well as written formats, makes key vocabulary accessible to a broader range of students and the interested public. Further, as Dawn E/PO has invited the public to learn about mission objectives as the mission explored asteroid Vesta, new inroads into public presentations such as the Dawn MissionCast tell the story of this extraordinary mission. Asteroid Mapper is the latest, exciting citizen science endeavor designed to invite the general public into the thrill of NASA science. Helping teachers develop a picture of the history and evolution of our understanding of the solar system, and honing in on the place of asteroids in helping us answer old questions and discover new ones, students and the general public sees the power and excitement underlying planetary science as human endeavor. Research indicates that science inquiry is powerful in the classroom and mission scientists are real-life models of science inquiry in action. Cross-curricular elements include examining research-based strategies for enhancing English language learners' ability to engage in higher order questions and a professional astronomy artist's insight into how visual analysis requires not just our eyes engaged, but our brains: comparing, synthesizing, questioning, evaluating, and wondering. Dawn Education and Public Outreach will share out perspectives and lessons learned, backed by extensive evaluation examining the efficacy of the mission's efforts.

Methods and Strategies:Students as Authors

ERIC Educational Resources Information Center

Varelas, Maria; Pappas, Christine C.; Kokkino, Sofia; Ortiz, Ibett

2008-01-01

Are you looking for ways to effectively integrate--and assess--science and literacy learning? Try having your students create their own books! The Integrated Science Literacy Enactments (ISLE) approach to teaching and learning science is one way to develop students' science understandings while simultaneously enhancing their communication skills.…

Back to the basic sciences: an innovative approach to teaching senior medical students how best to integrate basic science and clinical medicine.

PubMed

Spencer, Abby L; Brosenitsch, Teresa; Levine, Arthur S; Kanter, Steven L

2008-07-01

Abraham Flexner persuaded the medical establishment of his time that teaching the sciences, from basic to clinical, should be a critical component of the medical student curriculum, thus giving rise to the "preclinical curriculum." However, students' retention of basic science material after the preclinical years is generally poor. The authors believe that revisiting the basic sciences in the fourth year can enhance understanding of clinical medicine and further students' understanding of how the two fields integrate. With this in mind, a return to the basic sciences during the fourth year of medical school may be highly beneficial. The purpose of this article is to (1) discuss efforts to integrate basic science into the clinical years of medical student education throughout the United States and Canada, and (2) describe the highly developed fourth-year basic science integration program at the University of Pittsburgh School of Medicine. In their critical review of medical school curricula of 126 U.S. and 17 Canadian medical schools, the authors found that only 19% of U.S. medical schools and 24% of Canadian medical schools require basic science courses or experiences during the clinical years, a minor increase compared with 1985. Curricular methods ranged from simple lectures to integrated case studies with hands-on laboratory experience. The authors hope to advance the national discussion about the need to more fully integrate basic science teaching throughout all four years of the medical student curriculum by placing a curricular innovation in the context of similar efforts by other U.S. and Canadian medical schools.

Using the earth system for integrating the science curriculum

NASA Astrophysics Data System (ADS)

Mayer, Victor J.

Content and process instruction from the earth sciences has gone unrepresented in the world's science curricula, especially at the secondary level. As a result there is a serious deficiency in public understanding of the planet on which we all live. This lack includes national and international leaders in politics, business, and science. The earth system science effort now engaging the research talent of the earth sciences provides a firm foundation from the sciences for inclusion of earth systems content into the evolving integrated science curricula of this country and others. Implementing integrated science curricula, especially at the secondary level where potential leaders often have their only exposure to science, can help to address these problems. The earth system provides a conceptual theme as opposed to a disciplinary theme for organizing such integrated curricula, absent from prior efforts. The end of the cold war era is resulting in a reexamination of science and the influence it has had on our planet and society. In the future, science and the curricula that teach about science must seriously address the environmental and social problems left in the wake of over 100 years of preparation for military and economic war. The earth systems education effort provides one such approach to the modernization of science curricula. Earth science educators should assume leadership in helping to establish such curricula in this country and around the world.

Promoting Science and Technology in Primary Education: A Review of Integrated Curricula

ERIC Educational Resources Information Center

Gresnigt, Rens; Taconis, Ruurd; van Keulen, Hanno; Gravemeijer, Koeno; Baartman, Liesbeth

2014-01-01

Integrated curricula seem promising for the increase of attention on science and technology in primary education. A clear picture of the advantages and disadvantages of integration efforts could help curriculum innovation. This review has focused on integrated curricula in primary education from 1994 to 2011. The integrated curricula were…

Integration of a Communicating Science Module into an Advanced Chemistry Laboratory Course

ERIC Educational Resources Information Center

Renaud, Jessica; Squier, Christopher; Larsen, Sarah C.

2006-01-01

A communicating science module was introduced into an advanced undergraduate physical chemistry laboratory course. The module was integrated into the course such that students received formal instruction in communicating science interwoven with the chemistry laboratory curriculum. The content of the communicating science module included three…

Integration of Culturally Relevant Pedagogy into the Science Learning Progression Framework

ERIC Educational Resources Information Center

Bernardo, Cyntra

2017-01-01

This study integrated elements of culturally relevant pedagogy into a science learning progression framework, with the goal of enhancing teachers' cultural knowledge and thereby creating better teaching practices in an urban public high school science classroom. The study was conducted using teachers, an administrator, a science coach, and…

Preparation Model of Student Teacher Candidate in Developing Integrative Science Learning

ERIC Educational Resources Information Center

Wiyanto; Widiyatmoko, Arif

2016-01-01

According to 2013 Curriculum in Indonesia, science learning process in Junior High School is integrally held between physics, chemistry, biology, and earth science. To successfully implementing the 2013 Curriculum in school, the education institution which generates science teacher should prepare the student, so that they can develop integrative…

Integrating Engineering into an Urban Science Classroom

ERIC Educational Resources Information Center

Meyer, Helen

2017-01-01

This article presents a single case study of an experienced physical science teacher (Janet) integrating engineering practices into her urban science classroom over a two-year time frame. The article traces how Janet's understanding of the role engineering in her teaching expanded beyond engineering as an application of science and mathematics to…

Teachers' Voices on Integrating Metacognition into Science Education

ERIC Educational Resources Information Center

Ben-David, Adi; Orion, Nir

2013-01-01

This study is an attempt to gain new insight, on behalf of science teachers, into the integration of metacognition (MC) into science education. Participants were 44 elementary school science teachers attending an in-service teacher-training (INST) program. Data collection was carried out by several data sources: recordings of all verbal…

Integrating Mathematics, Science, and Language Arts Instruction Using the World Wide Web.

ERIC Educational Resources Information Center

Clark, Kenneth; Hosticka, Alice; Kent, Judi; Browne, Ron

1998-01-01

Addresses issues of access to World Wide Web sites, mathematics and science content-resources available on the Web, and methods for integrating mathematics, science, and language arts instruction. (Author/ASK)

Challenges and Support When Teaching Science Through an Integrated Inquiry and Literacy Approach

NASA Astrophysics Data System (ADS)

Ødegaard, Marianne; Haug, Berit; Mork, Sonja M.; Ove Sørvik, Gard

2014-12-01

In the Budding Science and Literacy project, we explored how working with an integrated inquiry-based science and literacy approach may challenge and support the teaching and learning of science at the classroom level. By studying the inter-relationship between multiple learning modalities and phases of inquiry, we wished to illuminate possible dynamics between science inquiry and literacy in an integrated science approach. Six teachers and their students were recruited from a professional development course for the current classroom study. The teachers were to try out the Budding Science teaching model. This paper presents an overall video analysis of our material demonstrating variations and patterns of inquiry-based science and literacy activities. Our analysis revealed that multiple learning modalities (read it, write it, do it, and talk it) are used in the integrated approach; oral activities dominate. The inquiry phases shifted throughout the students' investigations, but the consolidating phases of discussion and communication were given less space. The data phase of inquiry seems essential as a driving force for engaging in science learning in consolidating situations. The multiple learning modalities were integrated in all inquiry phases, but to a greater extent in preparation and data. Our results indicate that literacy activities embedded in science inquiry provide support for teaching and learning science; however, the greatest challenge for teachers is to find the time and courage to exploit the discussion and communication phases to consolidate the students' conceptual learning.

The European Bioinformatics Institute in 2017: data coordination and integration

PubMed Central

Cochrane, Guy; Apweiler, Rolf; Birney, Ewan

2018-01-01

Abstract The European Bioinformatics Institute (EMBL-EBI) supports life-science research throughout the world by providing open data, open-source software and analytical tools, and technical infrastructure (https://www.ebi.ac.uk). We accommodate an increasingly diverse range of data types and integrate them, so that biologists in all disciplines can explore life in ever-increasing detail. We maintain over 40 data resources, many of which are run collaboratively with partners in 16 countries (https://www.ebi.ac.uk/services). Submissions continue to increase exponentially: our data storage has doubled in less than two years to 120 petabytes. Recent advances in cellular imaging and single-cell sequencing techniques are generating a vast amount of high-dimensional data, bringing to light new cell types and new perspectives on anatomy. Accordingly, one of our main focus areas is integrating high-quality information from bioimaging, biobanking and other types of molecular data. This is reflected in our deep involvement in Open Targets, stewarding of plant phenotyping standards (MIAPPE) and partnership in the Human Cell Atlas data coordination platform, as well as the 2017 launch of the Omics Discovery Index. This update gives a birds-eye view of EMBL-EBI’s approach to data integration and service development as genomics begins to enter the clinic. PMID:29186510

A Framework for Addressing Skeptics' Claims Using Evidence-Based Argumentation: Lessons Learned from Educational Research

NASA Astrophysics Data System (ADS)

Lambert, J. L.; Bleicher, R. E.; Edwards, A.; Henderson, A.

2012-12-01

In science education, climate change is an issue that is especially useful for teaching concepts spanning several fields of science, as well the nature and practices of science. In response, we are developing a NASA-funded curriculum, titled Climate Science Investigations (CSI): South Florida, that teaches high school and first-year undergraduate level students how to analyze and use scientific data answer questions about climate change. To create an effective curriculum, we integrated lessons learned from our educational research conducted within our elementary science methods courses (Lambert, Lindgren, & Bleicher, 2012). For the past few years, we have been integrating climate science in our courses as a way to teach standards across several science disciplines and assessing our preservice teachers' gains in knowledge over the semesters. More recently, given the media attention and reports on the public's shift in opinion toward being more skeptical (Kellstedt, Zahran, & Vedlitz, 2008; Washington & Cook, 2011), we have assessed our students' perceptions about climate change and implemented strategies to help students use evidence-based scientific argumentation to address common claims of climate skeptics. In our elementary science methods courses, we framed climate change as a crosscutting theme, as well as a core idea, in the Next Generation Science Standards. We proposed that the issue and science of climate change would help preservice teachers not only become more interested in the topic, but also be more prepared to teach core science concepts spanning several disciplines (physical, life, and earth sciences). We also thought that highlighting the "practice of scientific inquiry" by teaching students to develop evidence-based arguments would help the preservice teachers become more analytical and able to differentiate scientific evidence from opinions, which could ultimately influence their perceptions on climate change. Lessons learned from our preservice teachers' conceptions and perceptions about climate change, as well as the difficulties in engaging in evidence-based argumentation, have informed and enhanced the framework for development of the CSI: South Florida curriculum. The modules are sequenced according to the proposed learning progression. First, students are introduced to the nature of science and Earth's energy balance. Students then investigate the temporal and spatial temperature data to answer the question of whether Earth is warming. Students also compare natural and anthropogenic causes of climate change, investigate the various observed and projected consequences of climate change in the fourth module, and examine ways to mitigate the effects of and adapt to climate change. Finally, students learn how to refute skeptics' claims by providing counter evidence and reasoning of why the skeptics' claim is not the appropriate explanation. This paper describes our conceptual framework for teaching students how to address the skeptics' claims using the content learned in the CSI: South Florida curriculum and evidence-based argumentation.

Genome Science: A Video Tour of the Washington University Genome Sequencing Center for High School and Undergraduate Students

ERIC Educational Resources Information Center

Flowers, Susan K.; Easter, Carla; Holmes, Andrea; Cohen, Brian; Bednarski, April E.; Mardis, Elaine R.; Wilson, Richard K.; Elgin, Sarah C. R.

2005-01-01

Sequencing of the human genome has ushered in a new era of biology. The technologies developed to facilitate the sequencing of the human genome are now being applied to the sequencing of other genomes. In 2004, a partnership was formed between Washington University School of Medicine Genome Sequencing Center's Outreach Program and Washington…

The Junior High School Integrated Science: The Actual Teaching Process in the Perspective of an Ethnographer

ERIC Educational Resources Information Center

Adu-Gyamfi, Kenneth; Ampiah, Joseph Ghartey

2016-01-01

Science education at the Basic School (Primary and Junior High School) serves as the foundation upon which higher levels of science education are pivoted. This ethnographic study sought to investigate the teaching of Integrated Science at the Junior High School (JHS) level in the classrooms of two science teachers in two schools of differing…

Integrating Reading into Middle School Science: What We Did, Found and Learned

ERIC Educational Resources Information Center

Fang, Zhihui; Lamme, Linda; Pringle, Rose; Patrick, Jennifer; Sanders, Jennifer; Zmach, Courtney; Charbonnet, Sara; Henkel, Melissa

2008-01-01

Recent calls for border crossing between reading and science have heightened the need to support science teachers in integrating reading into science and to verify the robustness of this approach in the context of inquiry-based science. In this paper, we share what we did, found, and learned in a collaborative project in which a team of…

Integrating Microcomputers into Science Education. Computer Technology Program Reports to Decision Makers. Number 6, November 1985.

ERIC Educational Resources Information Center

Batey, Anne

Computers are integrated into science education when they are used as the most appropriate tool or delivery system to support the goals of science education. The goals of science education can be condensed into two general areas. One area concerns the preparation of a science-literate citizenry; the second area concerns understanding the…

The Effects of Student Multiple Intelligence Preference on Integration of Earth Science Concepts and Knowledge within a Middle Grades Science Classroom.

ERIC Educational Resources Information Center

Cutshall, Lisa Christine

This research was conducted in an eastern Tennessee 8th grade science classroom with 99 students participating. The action research project attempted to examine an adolescent science student's integration of science concepts within a project-based setting using the multiple intelligence theory. In an effort to address the national science…

Science IA (Agriscience). A Science Credit for Agriculture: Integrating Academic and Vocational Education.

ERIC Educational Resources Information Center

Ricketts, Samuel C.

Because college-bound students often had trouble fitting agricultural education courses into their schedules, and because science teachers rejected the idea of giving a science credit for 2 years of agricultural education, a new integrated course was created in Tennessee. It is now called Science IA (Agriscience). It is taught by a teacher with an…

Extracting DNA words based on the sequence features: non-uniform distribution and integrity.

PubMed

Li, Zhi; Cao, Hongyan; Cui, Yuehua; Zhang, Yanbo

2016-01-25

DNA sequence can be viewed as an unknown language with words as its functional units. Given that most sequence alignment algorithms such as the motif discovery algorithms depend on the quality of background information about sequences, it is necessary to develop an ab initio algorithm for extracting the "words" based only on the DNA sequences. We considered that non-uniform distribution and integrity were two important features of a word, based on which we developed an ab initio algorithm to extract "DNA words" that have potential functional meaning. A Kolmogorov-Smirnov test was used for consistency test of uniform distribution of DNA sequences, and the integrity was judged by the sequence and position alignment. Two random base sequences were adopted as negative control, and an English book was used as positive control to verify our algorithm. We applied our algorithm to the genomes of Saccharomyces cerevisiae and 10 strains of Escherichia coli to show the utility of the methods. The results provide strong evidences that the algorithm is a promising tool for ab initio building a DNA dictionary. Our method provides a fast way for large scale screening of important DNA elements and offers potential insights into the understanding of a genome.

Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data.

PubMed

Kamboj, Atul; Hallwirth, Claus V; Alexander, Ian E; McCowage, Geoffrey B; Kramer, Belinda

2017-06-17

The analysis of viral vector genomic integration sites is an important component in assessing the safety and efficiency of patient treatment using gene therapy. Alongside this clinical application, integration site identification is a key step in the genetic mapping of viral elements in mutagenesis screens that aim to elucidate gene function. We have developed a UNIX-based vector integration site analysis pipeline (Ub-ISAP) that utilises a UNIX-based workflow for automated integration site identification and annotation of both single and paired-end sequencing reads. Reads that contain viral sequences of interest are selected and aligned to the host genome, and unique integration sites are then classified as transcription start site-proximal, intragenic or intergenic. Ub-ISAP provides a reliable and efficient pipeline to generate large datasets for assessing the safety and efficiency of integrating vectors in clinical settings, with broader applications in cancer research. Ub-ISAP is available as an open source software package at https://sourceforge.net/projects/ub-isap/ .

A synergistic effort among geoscience, physics, computer science and mathematics at Hunter College of CUNY as a Catalyst for educating Earth scientists.

NASA Astrophysics Data System (ADS)

Salmun, H.; Buonaiuto, F. S.

2016-12-01

The Catalyst Scholarship Program at Hunter College of The City University of New York (CUNY) was established with a four-year award from the National Science Foundation (NSF) to fund scholarships for academically talented but financially disadvantaged students majoring in four disciplines of science, technology, engineering and mathematics (STEM). Led by Earth scientists the Program awarded scholarships to students in their junior or senior years majoring in computer science, geosciences, mathematics and physics to create two cohorts of students that spent a total of four semesters in an interdisciplinary community. The program included mentoring of undergraduate students by faculty and graduate students (peer-mentoring), a sequence of three semesters of a one-credit seminar course and opportunities to engage in research activities, research seminars and other enriching academic experiences. Faculty and peer-mentoring were integrated into all parts of the scholarship activities. The one-credit seminar course, although designed to expose scholars to the diversity STEM disciplines and to highlight research options and careers in these disciplines, was thematically focused on geoscience, specifically on ocean and atmospheric science. The program resulted in increased retention rates relative to institutional averages. In this presentation we will discuss the process of establishing the program, from the original plans to its implementation, as well as the impact of this multidisciplinary approach to geoscience education at our institution and beyond. An overview of accomplishments, lessons learned and potential for best practices will be presented.

Mi-STAR: Designing Integrated Science Curriculum to Address the Next Generation Science Standards and Their Foundations

NASA Astrophysics Data System (ADS)

Gochis, E. E.; Huntoon, J. E.

2015-12-01

Mi-STAR (Michigan Science Teaching and Assessment Reform, http://mi-star.mtu.edu/) was funded by the Herbert H. and Grace A. Dow Foundation to reform K-12 science education to present science as an integrated body of knowledge that is applied to address societal issues. To achieve this goal, Mi-STAR is developing an integrated science curriculum for the middle grades that will be aligned with the Next Generation Science Standards (NGSS). Similar to the geosciences, the curriculum requires the integration of science, engineering and math content to explore 21st-century issues and demonstrates how these concepts can be used in service of society. The curriculum is based on the Mi-STAR Unit Specification Chart which pairs interdisciplinary themes with bundled NGSS Performance Expectations. Each unit is developed by a collaborative team of K-12 teachers, university STEM content experts and science education experts. Prior to developing a unit, each member on the team attends the on-line Mi-STAR Academy, completing 18+ hours of professional development (PD). This on-line PD program familiarizes teachers and experts with necessary pedagogical and content background knowledge, including NGSS and three-dimensional learning. With this background, teams use a staged, backwards design process to craft a multi-week unit based on a series of performance based tasks, or 'challenges' that engage students in actively doing science and engineering. Each unit includes Disciplinary Core Ideas from multiple disciplines, which focus on local and familiar examples that demonstrate the relevance of science in student's lives. Performance-based assessments are interwoven throughout the unit. Mi-STAR units will go through extensive pilot testing in several school districts across the state of Michigan. Additionally, the Mi-STAR program will develop teacher professional development programs to support implementation of the curriculum and design a pre-service teacher program in integrated science. We will share preliminary results on the collaborative Mi-STAR process of designing integrated science curriculum to address NGSS.

Teacher Design in Teams as a Professional Development Arrangement for Developing Technology Integration Knowledge and Skills of Science Teachers in Tanzania

ERIC Educational Resources Information Center

Kafyulilo, Ayoub; Fisser, Petra; Voogt, Joke

2016-01-01

This study investigated the impact of teacher design teams as a professional development arrangement for developing technology integration knowledge and skills among in-service science teachers. The study was conducted at a secondary school in Tanzania, where 12 in-service science teachers participated in a workshop about technology integration in…

A Longitudinal Look at Attitudes and Perceptions Related to the Integration of Mathematics, Science, and Technology Education

ERIC Educational Resources Information Center

Berlin, Donna F.; White, Arthur L.

2012-01-01

The purpose of this study is to provide an in-depth analysis of attitudes and perceptions related to the integration of mathematics, science, and technology education of preservice teachers preparing to teach STEM disciplines. Longitudinal data by individual cohort and across 7 years of the Integrated Mathematics, Science, and Technology (MSAT)…

Gardening for Homonyms: Integrating Science and Language Arts to Support Children's Creative Use of Multiple Meaning Words

ERIC Educational Resources Information Center

Luna, Melissa J.; Rye, James Andrew; Forinash, Melissa; Minor, Alana

2015-01-01

Curriculum integration can increase the presence of science at the elementary level. The purpose of this article is to share how two second-grade teachers have integrated language arts content as a part of science-language arts instruction in a garden-based learning context. One application was a teacher-designed "Gardening for Homonyms"…

Personality Theories Facilitate Integrating the Five Principles and Deducing Hypotheses for Testing

ERIC Educational Resources Information Center

Maddi, Salvatore R.

2007-01-01

Comments on the original article "A New Big Five: Fundamental Principles for an Integrative Science of Personality," by Dan P. McAdams and Jennifer L. Pals (see record 2006-03947-002). In presenting their view of personality science, McAdams and Pals (April 2006) elaborated the importance of five principles for building an integrated science of…

Driven by Beliefs: Understanding Challenges Physical Science Teachers Face When Integrating Engineering and Physics

ERIC Educational Resources Information Center

Dare, Emily A.; Ellis, Joshua A.; Roehrig, Gillian H.

2014-01-01

It is difficult to ignore the increased use of technological innovations in today's world, which has led to various calls for the integration of engineering into K-12 science standards. The need to understand how engineering is currently being brought to science classrooms is apparent and necessary in order to address these calls for integration.…

Integrating Science, Technology, Engineering, and Mathematics: Issues, Reflections, and Ways Forward. Teaching and Learning in Science Series

ERIC Educational Resources Information Center

Rennie, Leonie, Ed.; Venville, Grady, Ed.; Wallace, John, Ed.

2012-01-01

How can curriculum integration of school science with the related disciplines of technology, engineering and mathematics (STEM) enhance students' skills and their ability to link what they learn in school with the world outside the classroom? Featuring actual case studies of teachers' attempts to integrate their curriculum, their reasons for doing…

Schemes for Integrating Text and Image in the Science Textbook: Effects on Comprehension and Situational Interest

ERIC Educational Resources Information Center

Peterson, Matthew O.

2016-01-01

Science education researchers have turned their attention to the use of images in textbooks, both because pages are heavily illustrated and because visual literacy is an important aptitude for science students. Text-image integration in the textbook is described here as composition schemes in increasing degrees of integration: prose primary (PP),…

Status of the JWST Integrated Science Instrument Module

NASA Astrophysics Data System (ADS)

Greenhouse, Matthew A.; Dunn, Jamie; Kimble, Randy A.; Lambros, Scott; Lundquist, Ray; Rauscher, Bernard J.; Van Campen, Julie

2015-01-01

The James Webb Space Telescope (JWST) Integrated Science Instrument Module (ISIM) is the science instrument payload of the JWST. It is one of three system elements that comprise the JWST space vehicle. It consists of four science sensors, a fine guidance sensor, and nine other subsystems that support them. At 1.4 metric tons, it comprises approximately 20% of the JWST mass. The ISIM is currently at 100% integration and has completed 2 of 3 planned element-level space simulation tests. The ISIM is on schedule to be delivered for integration with the Optical Telescope Element during 2015. In this poster, we present an overview of the ISIM and its status.

Investigation of modulation parameters in multiplexing gas chromatography.

PubMed

Trapp, Oliver

2010-10-22

Combination of information technology and separation sciences opens a new avenue to achieve high sample throughputs and therefore is of great interest to bypass bottlenecks in catalyst screening of parallelized reactors or using multitier well plates in reaction optimization. Multiplexing gas chromatography utilizes pseudo-random injection sequences derived from Hadamard matrices to perform rapid sample injections which gives a convoluted chromatogram containing the information of a single sample or of several samples with similar analyte composition. The conventional chromatogram is obtained by application of the Hadamard transform using the known injection sequence or in case of several samples an averaged transformed chromatogram is obtained which can be used in a Gauss-Jordan deconvolution procedure to obtain all single chromatograms of the individual samples. The performance of such a system depends on the modulation precision and on the parameters, e.g. the sequence length and modulation interval. Here we demonstrate the effects of the sequence length and modulation interval on the deconvoluted chromatogram, peak shapes and peak integration for sequences between 9-bit (511 elements) and 13-bit (8191 elements) and modulation intervals Δt between 5 s and 500 ms using a mixture of five components. It could be demonstrated that even for high-speed modulation at time intervals of 500 ms the chromatographic information is very well preserved and that the separation efficiency can be improved by very narrow sample injections. Furthermore this study shows that the relative peak areas in multiplexed chromatograms do not deviate from conventionally recorded chromatograms. Copyright © 2010 Elsevier B.V. All rights reserved.

Plastome Sequencing of Ten Nonmodel Crop Species Uncovers a Large Insertion of Mitochondrial DNA in Cashew.

PubMed

Rabah, Samar O; Lee, Chaehee; Hajrah, Nahid H; Makki, Rania M; Alharby, Hesham F; Alhebshi, Alawiah M; Sabir, Jamal S M; Jansen, Robert K; Ruhlman, Tracey A

2017-11-01

In plant evolution, intracellular gene transfer (IGT) is a prevalent, ongoing process. While nuclear and mitochondrial genomes are known to integrate foreign DNA via IGT and horizontal gene transfer (HGT), plastid genomes (plastomes) have resisted foreign DNA incorporation and only recently has IGT been uncovered in the plastomes of a few land plants. In this study, we completed plastome sequences for l0 crop species and describe a number of structural features including variation in gene and intron content, inversions, and expansion and contraction of the inverted repeat (IR). We identified a putative in cinnamon ( J. Presl) and other sequenced Lauraceae and an apparent functional transfer of to the nucleus of quinoa ( Willd.). In the orchard tree cashew ( L.), we report the insertion of an ∼6.7-kb fragment of mitochondrial DNA into the plastome IR. BLASTn analyses returned high identity hits to mitogenome sequences including an intact open reading frame. Using three plastome markers for five species of , we generated a phylogeny to investigate the distribution and timing of the insertion. Four species share the insertion, suggesting that this event occurred <20 million yr ago in a single clade in the genus. Our study extends the observation of mitochondrial to plastome IGT to include long-lived tree species. While previous studies have suggested possible mechanisms facilitating IGT to the plastome, more examples of this phenomenon, along with more complete mitogenome sequences, will be required before a common, or variable, mechanism can be elucidated. Copyright © 2017 Crop Science Society of America.

Examining the effect of self-explanation on cognitive integration of basic and clinical sciences in novices.

PubMed

Lisk, Kristina; Agur, Anne M R; Woods, Nicole N

2017-12-01

Several studies have shown that cognitive integration of basic and clinical sciences supports diagnostic reasoning in novices; however, there has been limited exploration of the ways in which educators can translate this model of mental activity into sound instructional strategies. The use of self-explanation during learning has the potential to promote and support the development of integrated knowledge by encouraging novices to elaborate on the causal relationship between clinical features and basic science mechanisms. To explore the effect of this strategy, we compared diagnostic efficacy of teaching students (n = 71) the clinical features of four musculoskeletal pathologies using either (1) integrated causal basic science descriptions (BaSci group); (2) integrated causal basic science descriptions combined with self-explanation prompts (SE group); (3) basic science mechanisms segregated from the clinical features (SG group). All participants completed a diagnostic accuracy test immediately after learning and 1-week later. The results showed that the BaSci group performed significantly better compared to the SE (p = 0.019) and SG groups (p = 0.004); however, no difference was observed between the SE and SG groups (p = 0.91). We hypothesize that the structure of the self-explanation task may not have supported the development of a holistic conceptual understanding of each disease. These findings suggest that integration strategies need to be carefully structured and applied in ways that support the holistic story created by integrated basic science instruction in order to foster conceptual coherence and to capitalize on the benefits of cognition integration.

Clonal Evaluation of Prostate Cancer by ERG/SPINK1 Status to Improve Prognosis Prediction

DTIC Science & Technology

2016-10-01

clinical oncology , cancer genetics, genomic science/bioinformatics, clinical pathology, social and behavioral sciences, and bioethics in order to...Interpret and translate sequence variants into clinical oncology setting; 5) Assess and evaluate costs associated with clinical sequencing. Role...Lethal Prostate Cancer Goal(s): Radiation Therapy Oncology Group (RTOG) 96-01 represents a phase III trial of of salvage radiation therapy (RT) alone

Recent Seismicity in Texas and Research Design and Progress of the TexNet-CISR Collaboration

NASA Astrophysics Data System (ADS)

Hennings, P.; Savvaidis, A.; Rathje, E.; Olson, J. E.; DeShon, H. R.; Datta-Gupta, A.; Eichhubl, P.; Nicot, J. P.; Kahlor, L. A.

2017-12-01

The recent increase in the rate of seismicity in Texas has prompted the establishment of an interdisciplinary, interinstitutional collaboration led by the Texas Bureau of Economic Geology which includes the TexNet Seismic Monitoring and Research project as funded by The State of Texas (roughly 2/3rds of our funding) and the industry-funded Center for Integrated Seismicity Research (CISR) (1/3 of funding). TexNet is monitoring and cataloging seismicity across Texas using a new backbone seismic network, investigating site-specific earthquake sequences by deploying temporary seismic monitoring stations, and conducting reservoir modeling studies. CISR expands TexNet research into the interdisciplinary realm to more thoroughly study the factors that contribute to seismicity, characterize the associated hazard and risk, develop strategies for mitigation and management, and develop methods of effective communication for all stakeholders. The TexNet-CISR research portfolio has 6 themes: seismicity monitoring, seismology, geologic and hydrologic description, geomechanics and reservoir modeling, seismic hazard and risk assessment, and seismic risk social science. Twenty+ specific research projects span and connect these themes. We will provide a synopsis of research progress including recent seismicity trends in Texas; Fort Worth Basin integrated studies including geological modeling and fault characterization, fluid injection data syntheses, and reservoir and geomechanical modeling; regional ground shaking characterization and mapping, infrastructure vulnerability assessment; and social science topics of public perception and information seeking behavior.

INTEGRATED SCIENCE FOR ECOSYSTEM CHALLENGES - ISEC

EPA Science Inventory

In support of the National Science and Technology Council's cross-Agency priority of Integrated Science for Ecological Challenges (ISEC) EPA is conducting research to improve capabilities in the area of regional vulnerability assessment and ecological forecasting. EPA's research...

The NASA Science Internet: An integrated approach to networking

NASA Technical Reports Server (NTRS)

Rounds, Fred

1991-01-01

An integrated approach to building a networking infrastructure is an absolute necessity for meeting the multidisciplinary science networking requirements of the Office of Space Science and Applications (OSSA) science community. These networking requirements include communication connectivity between computational resources, databases, and library systems, as well as to other scientists and researchers around the world. A consolidated networking approach allows strategic use of the existing science networking within the Federal government, and it provides networking capability that takes into consideration national and international trends towards multivendor and multiprotocol service. It also offers a practical vehicle for optimizing costs and maximizing performance. Finally, and perhaps most important to the development of high speed computing is that an integrated network constitutes a focus for phasing to the National Research and Education Network (NREN). The NASA Science Internet (NSI) program, established in mid 1988, is structured to provide just such an integrated network. A description of the NSI is presented.

A study of the continuum of integration of mathematics content with science concepts at the middle school level in West Virginia

NASA Astrophysics Data System (ADS)

Meisel, Edna Marie

The purpose of this study was to examine the practices and perceptions of regular education seventh grade middle school mathematics teachers in West Virginia concerning the integration of mathematics objectives with science concepts. In addition, this study also emphasized the use of integrated curriculum continuum models to study mathematics teachers' practices and perceptions for teaching mathematics objectives in connection with science concepts. It was argued that the integrated curriculum continuum model can be used to help educators begin to form a common definition of integrated curriculum. The population was described as the regular education seventh grade middle school mathematics teachers in West Virginia. The entire population (N = 173) was used as the participants in this study. Data was collected using an integrated curriculum practices and perceptions survey constructed by the researcher. This was a descriptive study that incorporated the Chi Square statistic to show trends in teacher practices and perceptions. Also, an ex post facto design, that incorporated the Mann-Whitney U statistic, was used to compare practices and perceptions between teachers grouped according to factors that influence teaching practices and perceptions. These factors included teaching certificate endorsement and teacher professional preparation. Results showed that the regular education seventh grade middle school mathematics teachers of West Virginia are teaching mathematics objectives mainly at a discipline-based level with no formal attempt for integration with science concepts. However, these teachers perceived that many of the mathematics objectives should be taught at varying levels of integration with science concepts. It was also shown that teachers who experienced professional preparation courses that emphasized integrated curriculum courses did teach many of the mathematics objectives at higher levels of integration with science than those teachers who did not experience integrated curriculum courses.

Soil DNA metabarcoding and high-throughput sequencing as a forensic tool: considerations, potential limitations and recommendations.

PubMed

Young, J M; Austin, J J; Weyrich, L S

2017-02-01

Analysis of physical evidence is typically a deciding factor in forensic casework by establishing what transpired at a scene or who was involved. Forensic geoscience is an emerging multi-disciplinary science that can offer significant benefits to forensic investigations. Soil is a powerful, nearly 'ideal' contact trace evidence, as it is highly individualistic, easy to characterise, has a high transfer and retention probability, and is often overlooked in attempts to conceal evidence. However, many real-life cases encounter close proximity soil samples or soils with low inorganic content, which cannot be easily discriminated based on current physical and chemical analysis techniques. The capability to improve forensic soil discrimination, and identify key indicator taxa from soil using the organic fraction is currently lacking. The development of new DNA sequencing technologies offers the ability to generate detailed genetic profiles from soils and enhance current forensic soil analyses. Here, we discuss the use of DNA metabarcoding combined with high-throughput sequencing (HTS) technology to distinguish between soils from different locations in a forensic context. Specifically, we provide recommendations for best practice, outline the potential limitations encountered in a forensic context and describe the future directions required to integrate soil DNA analysis into casework. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

[Boundaries and integrity in the "Social Contract for Spanish Science", 1907-1939].

PubMed

Gómez, Amparo

2014-01-01

This article analyzes the relationship between science and politics in Spain in the early 20th century from the perspective of the Social Contract for Science. The article shows that a genuine social contract for science was instituted in Spain during this period, although some boundary and integrity problems emerged. These problems are analyzed, showing that the boundary problems were a product of the conservative viewpoint on the relationship between science and politics, while the integrity problems involved the activation of networks of influence in the awarding of scholarships to study abroad. Finally, the analysis reveals that these problems did not invalidate the Spanish social contract for science.

The use of simulation in teaching the basic sciences.

PubMed

Eason, Martin P

2013-12-01

To assess the current use of simulation in medical education, specifically, the teaching of the basic sciences to accomplish the goal of improved integration. Simulation is increasingly being used by the institutions to teach the basic sciences. Preliminary data suggest that it is an effective tool with increased retention and learner satisfaction. Medical education is undergoing tremendous change. One of the directions of that change is increasing integration of the basic and clinical sciences to improve the efficiency and quality of medical education, and ultimately to improve the patient care. Integration is thought to improve the understanding of basic science conceptual knowledge and to better prepare the learners for clinical practice. Simulation because of its unique effects on learning is currently being successfully used by many institutions as a means to produce that integration through its use in the teaching of the basic sciences. Preliminary data indicate that simulation is an effective tool for basic science education and garners high learner satisfaction.

An Integrated SNP Mining and Utilization (ISMU) Pipeline for Next Generation Sequencing Data

PubMed Central

Azam, Sarwar; Rathore, Abhishek; Shah, Trushar M.; Telluri, Mohan; Amindala, BhanuPrakash; Ruperao, Pradeep; Katta, Mohan A. V. S. K.; Varshney, Rajeev K.

2014-01-01

Open source single nucleotide polymorphism (SNP) discovery pipelines for next generation sequencing data commonly requires working knowledge of command line interface, massive computational resources and expertise which is a daunting task for biologists. Further, the SNP information generated may not be readily used for downstream processes such as genotyping. Hence, a comprehensive pipeline has been developed by integrating several open source next generation sequencing (NGS) tools along with a graphical user interface called Integrated SNP Mining and Utilization (ISMU) for SNP discovery and their utilization by developing genotyping assays. The pipeline features functionalities such as pre-processing of raw data, integration of open source alignment tools (Bowtie2, BWA, Maq, NovoAlign and SOAP2), SNP prediction (SAMtools/SOAPsnp/CNS2snp and CbCC) methods and interfaces for developing genotyping assays. The pipeline outputs a list of high quality SNPs between all pairwise combinations of genotypes analyzed, in addition to the reference genome/sequence. Visualization tools (Tablet and Flapjack) integrated into the pipeline enable inspection of the alignment and errors, if any. The pipeline also provides a confidence score or polymorphism information content value with flanking sequences for identified SNPs in standard format required for developing marker genotyping (KASP and Golden Gate) assays. The pipeline enables users to process a range of NGS datasets such as whole genome re-sequencing, restriction site associated DNA sequencing and transcriptome sequencing data at a fast speed. The pipeline is very useful for plant genetics and breeding community with no computational expertise in order to discover SNPs and utilize in genomics, genetics and breeding studies. The pipeline has been parallelized to process huge datasets of next generation sequencing. It has been developed in Java language and is available at http://hpc.icrisat.cgiar.org/ISMU as a standalone free software. PMID:25003610

E-MSD: an integrated data resource for bioinformatics.

PubMed

Velankar, S; McNeil, P; Mittard-Runte, V; Suarez, A; Barrell, D; Apweiler, R; Henrick, K

2005-01-01

The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the worldwide Protein Data Bank (wwPDB) and to work towards the integration of various bioinformatics data resources. One of the major obstacles to the improved integration of structural databases such as MSD and sequence databases like UniProt is the absence of up to date and well-maintained mapping between corresponding entries. We have worked closely with the UniProt group at the EBI to clean up the taxonomy and sequence cross-reference information in the MSD and UniProt databases. This information is vital for the reliable integration of the sequence family databases such as Pfam and Interpro with the structure-oriented databases of SCOP and CATH. This information has been made available to the eFamily group (http://www.efamily.org.uk/) and now forms the basis of the regular interchange of information between the member databases (MSD, UniProt, Pfam, Interpro, SCOP and CATH). This exchange of annotation information has enriched the structural information in the MSD database with annotation from wider sequence-oriented resources. This work was carried out under the 'Structure Integration with Function, Taxonomy and Sequences (SIFTS)' initiative (http://www.ebi.ac.uk/msd-srv/docs/sifts) in the MSD group.

The Human Microbiome and Understanding the 16S rRNA Gene in Translational Nursing Science.

PubMed

Ames, Nancy J; Ranucci, Alexandra; Moriyama, Brad; Wallen, Gwenyth R

As more is understood regarding the human microbiome, it is increasingly important for nurse scientists and healthcare practitioners to analyze these microbial communities and their role in health and disease. 16S rRNA sequencing is a key methodology in identifying these bacterial populations that has recently transitioned from use primarily in research to having increased utility in clinical settings. The objectives of this review are to (a) describe 16S rRNA sequencing and its role in answering research questions important to nursing science; (b) provide an overview of the oral, lung, and gut microbiomes and relevant research; and (c) identify future implications for microbiome research and 16S sequencing in translational nursing science. Sequencing using the 16S rRNA gene has revolutionized research and allowed scientists to easily and reliably characterize complex bacterial communities. This type of research has recently entered the clinical setting, one of the best examples involving the use of 16S sequencing to identify resistant pathogens, thereby improving the accuracy of bacterial identification in infection control. Clinical microbiota research and related requisite methods are of particular relevance to nurse scientists-individuals uniquely positioned to utilize these techniques in future studies in clinical settings.

Ozone and Interdisciplinary Science Teaching--Learning to Address the Things That Count Most.

ERIC Educational Resources Information Center

Hobson, Art

1993-01-01

Presents the ozone depletion story as an excellent case study for the integration of science-related social issues into the college science curriculum. Describes the history of ozone depletion and efforts to remedy the problem. Provides a lecture outline on ozone depletion. Discusses integrating other science-related interdisciplinary topics in…

Research Directions in Remote Detection of Covert Tactical Adversarial Intent of Individuals in Asymmetric Operations

DTIC Science & Technology

2010-07-01

To be successful, the research needs to integrate kinesiological , neurophysiological, psychological, and cognitive science, and sociocultural... kinesiological neurophysiological, psychological, and cognitive science and sociocultural anthropology and information science components. Research and...successful, the research needs to integrate kinesiological , neurophysiological, psychological, and cognitive science, and sociocultural

Designing and Implementing an Integrated Technological Pedagogical Science Knowledge Framework for Science Teachers Professional Development

ERIC Educational Resources Information Center

Jimoyiannis, Athanassios

2010-01-01

This paper reports on the design and the implementation of the Technological Pedagogical Science Knowledge (TPASK), a new model for science teachers professional development built on an integrated framework determined by the Technological Pedagogical Content Knowledge (TPACK) model and the authentic learning approach. The TPASK curriculum…

STEM Integration in Middle School Life Science: Student Learning and Attitudes

ERIC Educational Resources Information Center

Guzey, S. Selcen; Moore, Tamara J.; Harwell, Michael; Moreno, Mario

2016-01-01

In many countries around the world, there has been an increasing emphasis on improving science education. Recent reform efforts in the USA call for teachers to integrate scientific and engineering practices into science teaching; for example, science teachers are asked to provide learning experiences for students that apply crosscutting concepts…

Learning Science by Engaging Religion: A Novel Two-Course Approach for Biology Majors

ERIC Educational Resources Information Center

Eisen, Arri; Huang, Junjian

2014-01-01

Many issues in science create individual and societal tensions with important implications outside the classroom. We describe one model that directly addresses such tensions by integrating science and religion in two parallel, integrated courses for science majors. Evaluation of the goals of the project--(1) providing students with strategies to…

A Truth-Based Epistemological Framework for Supporting Teachers in Integrating Indigenous Knowledge into Science Teaching

ERIC Educational Resources Information Center

Zinyeka, Gracious; Onwu, Gilbert O.M.; Braun, Max

2016-01-01

Integrating indigenous knowledge (IK) into school science teaching is one way of maximising the socio-cultural relevance of science education for enhanced learners' performance. The epistemological differences however between the nature of science (NOS) and nature of indigenous knowledge (NOIK) constitute a major challenge for an inclusive…

The Information Book Genre: Its Role in Integrated Science Literacy Research and Practice

ERIC Educational Resources Information Center

Pappas, Christine C.

2006-01-01

There has been a call for approaches that connect science learning with literacy, yet the use of, and research on, children's literature information books in science instruction has been quite limited. Because the discipline of science involves distinctive generic linguistic registers, what information books should be integrated in science…

Guiding Students towards Sensemaking: Teacher Questions Focused on Integrating Scientific Practices with Science Content

ERIC Educational Resources Information Center

Benedict-Chambers, Amanda; Kademian, Sylvie M.; Davis, Elizabeth A.; Palincsar, Annemarie Sullivan

2017-01-01

Science education reforms articulate a vision of ambitious science teaching where teachers engage students in sensemaking discussions and emphasise the integration of scientific practices with science content. Learning to teach in this way is complex, and there are few examples of sensemaking discussions in schools where textbook lessons and…

Supporting Kindergartners' Science Talk in the Context of an Integrated Science and Disciplinary Literacy Curriculum

ERIC Educational Resources Information Center

Wright, Tanya S.; Gotwals, Amelia Wenk

2017-01-01

Given the growing evidence of limited attention to science, disciplinary literacy, and oral language in elementary classrooms serving low-income children, this study focused on designing and testing an integrated science and disciplinary language and literacy curriculum aligned with NGSS and CCSS ELA standards for kindergarten. We used…

"Polymeromics": Mass spectrometry based strategies in polymer science toward complete sequencing approaches: a review.

PubMed

Altuntaş, Esra; Schubert, Ulrich S

2014-01-15

Mass spectrometry (MS) is the most versatile and comprehensive method in "OMICS" sciences (i.e. in proteomics, genomics, metabolomics and lipidomics). The applications of MS and tandem MS (MS/MS or MS(n)) provide sequence information of the full complement of biological samples in order to understand the importance of the sequences on their precise and specific functions. Nowadays, the control of polymer sequences and their accurate characterization is one of the significant challenges of current polymer science. Therefore, a similar approach can be very beneficial for characterizing and understanding the complex structures of synthetic macromolecules. MS-based strategies allow a relatively precise examination of polymeric structures (e.g. their molar mass distributions, monomer units, side chain substituents, end-group functionalities, and copolymer compositions). Moreover, tandem MS offer accurate structural information from intricate macromolecular structures; however, it produces vast amount of data to interpret. In "OMICS" sciences, the software application to interpret the obtained data has developed satisfyingly (e.g. in proteomics), because it is not possible to handle the amount of data acquired via (tandem) MS studies on the biological samples manually. It can be expected that special software tools will improve the interpretation of (tandem) MS output from the investigations of synthetic polymers as well. Eventually, the MS/MS field will also open up for polymer scientists who are not MS-specialists. In this review, we dissect the overall framework of the MS and MS/MS analysis of synthetic polymers into its key components. We discuss the fundamentals of polymer analyses as well as recent advances in the areas of tandem mass spectrometry, software developments, and the overall future perspectives on the way to polymer sequencing, one of the last Holy Grail in polymer science. Copyright © 2013 Elsevier B.V. All rights reserved.

SciBox, an end-to-end automated science planning and commanding system

NASA Astrophysics Data System (ADS)

Choo, Teck H.; Murchie, Scott L.; Bedini, Peter D.; Steele, R. Josh; Skura, Joseph P.; Nguyen, Lillian; Nair, Hari; Lucks, Michael; Berman, Alice F.; McGovern, James A.; Turner, F. Scott

2014-01-01

SciBox is a new technology for planning and commanding science operations for Earth-orbital and planetary space missions. It has been incrementally developed since 2001 and demonstrated on several spaceflight projects. The technology has matured to the point that it is now being used to plan and command all orbital science operations for the MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) mission to Mercury. SciBox encompasses the derivation of observing sequences from science objectives, the scheduling of those sequences, the generation of spacecraft and instrument commands, and the validation of those commands prior to uploading to the spacecraft. Although the process is automated, science and observing requirements are incorporated at each step by a series of rules and parameters to optimize observing opportunities, which are tested and validated through simulation and review. Except for limited special operations and tests, there is no manual scheduling of observations or construction of command sequences. SciBox reduces the lead time for operations planning by shortening the time-consuming coordination process, reduces cost by automating the labor-intensive processes of human-in-the-loop adjudication of observing priorities, reduces operations risk by systematically checking constraints, and maximizes science return by fully evaluating the trade space of observing opportunities to meet MESSENGER science priorities within spacecraft recorder, downlink, scheduling, and orbital-geometry constraints.

Exploring Ivorian Perspectives on the Effectiveness of the Current Ivorian Science Curriculum in Addressing Issues Related to HIV/AIDS

ERIC Educational Resources Information Center

Ado, Gustave Firmin

2014-01-01

School-based HIV/AIDS science education has the potential to impact students when integrated into the science curriculum. However, this mixed method study shows that school-based HIV/AIDS science education is often not infused into career subjects such as science education but integrated into civics education and taught by teachers who lack the…

Grand challenges for integrated USGS science—A workshop report

USGS Publications Warehouse

Jenni, Karen E.; Goldhaber, Martin B.; Betancourt, Julio L.; Baron, Jill S.; Bristol, R. Sky; Cantrill, Mary; Exter, Paul E.; Focazio, Michael J.; Haines, John W.; Hay, Lauren E.; Hsu, Leslie; Labson, Victor F.; Lafferty, Kevin D.; Ludwig, Kristin A.; Milly, Paul C. D.; Morelli, Toni L.; Morman, Suzette A.; Nassar, Nedal T.; Newman, Timothy R.; Ostroff, Andrea C.; Read, Jordan S.; Reed, Sasha C.; Shapiro, Carl D.; Smith, Richard A.; Sanford, Ward E.; Sohl, Terry L.; Stets, Edward G.; Terando, Adam J.; Tillitt, Donald E.; Tischler, Michael A.; Toccalino, Patricia L.; Wald, David J.; Waldrop, Mark P.; Wein, Anne; Weltzin, Jake F.; Zimmerman, Christian E.

2017-06-30

Executive SummaryThe U.S. Geological Survey (USGS) has a long history of advancing the traditional Earth science disciplines and identifying opportunities to integrate USGS science across disciplines to address complex societal problems. The USGS science strategy for 2007–2017 laid out key challenges in disciplinary and interdisciplinary arenas, culminating in a call for increased focus on a number of crosscutting science directions. Ten years on, to further the goal of integrated science and at the request of the Executive Leadership Team (ELT), a workshop with three dozen invited scientists spanning different disciplines and career stages in the Bureau convened on February 7–10, 2017, at the USGS John Wesley Powell Center for Analysis and Synthesis in Fort Collins, Colorado.The workshop focused on identifying “grand challenges” for integrated USGS science. Individual participants identified nearly 70 potential grand challenges before the workshop and through workshop discussions. After discussion, four overarching grand challenges emerged:Natural resource security,Societal risk from existing and emerging threats,Smart infrastructure development, andAnticipatory science for changing landscapes.Participants also identified a “comprehensive science challenge” that highlights the development of integrative science, data, models, and tools—all interacting in a modular framework—that can be used to address these and other future grand challenges:Earth Monitoring, Analyses, and Projections (EarthMAP)EarthMAP is our long-term vision for an integrated scientific framework that spans traditional scientific boundaries and disciplines, and integrates the full portfolio of USGS science: research, monitoring, assessment, analysis, and information delivery.The Department of Interior, and the Nation in general, have a vast array of information needs. The USGS meets these needs by having a broadly trained and agile scientific workforce. Encouraging and supporting cross-discipline engagement would position the USGS to tackle complex and multifaceted scientific and societal challenges in the 21st Century.

ISEES: an institute for sustainable software to accelerate environmental science

NASA Astrophysics Data System (ADS)

Jones, M. B.; Schildhauer, M.; Fox, P. A.

2013-12-01

Software is essential to the full science lifecycle, spanning data acquisition, processing, quality assessment, data integration, analysis, modeling, and visualization. Software runs our meteorological sensor systems, our data loggers, and our ocean gliders. Every aspect of science is impacted by, and improved by, software. Scientific advances ranging from modeling climate change to the sequencing of the human genome have been rendered possible in the last few decades due to the massive improvements in the capabilities of computers to process data through software. This pivotal role of software in science is broadly acknowledged, while simultaneously being systematically undervalued through minimal investments in maintenance and innovation. As a community, we need to embrace the creation, use, and maintenance of software within science, and address problems such as code complexity, openness,reproducibility, and accessibility. We also need to fully develop new skills and practices in software engineering as a core competency in our earth science disciplines, starting with undergraduate and graduate education and extending into university and agency professional positions. The Institute for Sustainable Earth and Environmental Software (ISEES) is being envisioned as a community-driven activity that can facilitate and galvanize activites around scientific software in an analogous way to synthesis centers such as NCEAS and NESCent that have stimulated massive advances in ecology and evolution. We will describe the results of six workshops (Science Drivers, Software Lifecycles, Software Components, Workforce Development and Training, Sustainability and Governance, and Community Engagement) that have been held in 2013 to envision such an institute. We will present community recommendations from these workshops and our strategic vision for how ISEES will address the technical issues in the software lifecycle, sustainability of the whole software ecosystem, and the critical issue of computational training for the scientific community. Process for envisioning ISEES.

An overview of human genetic privacy

PubMed Central

Shi, Xinghua; Wu, Xintao

2016-01-01

The study of human genomics is becoming a Big Data science, owing to recent biotechnological advances leading to availability of millions of personal genome sequences, which can be combined with biometric measurements from mobile apps and fitness trackers, and of human behavior data monitored from mobile devices and social media. With increasing research opportunities for integrative genomic studies through data sharing, genetic privacy emerges as a legitimate yet challenging concern that needs to be carefully addressed, not only for individuals but also for their families. In this paper, we present potential genetic privacy risks and relevant ethics and regulations for sharing and protecting human genomics data. We also describe the techniques for protecting human genetic privacy from three broad perspectives: controlled access, differential privacy, and cryptographic solutions. PMID:27626905

Making mathematics and science integration happen: key aspects of practice

NASA Astrophysics Data System (ADS)

Ríordáin, Máire Ní; Johnston, Jennifer; Walshe, Gráinne

2016-02-01

The integration of mathematics and science teaching and learning facilitates student learning, engagement, motivation, problem-solving, criticality and real-life application. However, the actual implementation of an integrative approach to the teaching and learning of both subjects at classroom level, with in-service teachers working collaboratively, at second-level education, is under-researched due to the complexities of school-based research. This study reports on a year-long case study on the implementation of an integrated unit of learning on distance, speed and time, within three second-level schools in Ireland. This study employed a qualitative approach and examined the key aspects of practice that impact on the integration of mathematics and science teaching and learning. We argue that teacher perspective, teacher knowledge of the 'other subject' and of technological pedagogical content knowledge (TPACK), and teacher collaboration and support all impact on the implementation of an integrative approach to mathematics and science education.

RNAcentral: an international database of ncRNA sequences

DOE PAGES

Williams, Kelly Porter

2014-10-28

The field of non-coding RNA biology has been hampered by the lack of availability of a comprehensive, up-to-date collection of accessioned RNA sequences. Here we present the first release of RNAcentral, a database that collates and integrates information from an international consortium of established RNA sequence databases. The initial release contains over 8.1 million sequences, including representatives of all major functional classes. A web portal (http://rnacentral.org) provides free access to data, search functionality, cross-references, source code and an integrated genome browser for selected species.

Mars Pathfinder flight system integration and test.

NASA Astrophysics Data System (ADS)

Muirhead, B. K.

This paper describes the system integration and test experiences, problems and lessons learned during the assembly, test and launch operations (ATLO) phase of the Mars Pathfinder flight system scheduled to land on the surface of Mars on July 4, 1997. The Mars Pathfinder spacecraft consists of three spacecraft systems: cruise stage, entry vehicle and lander. The cruise stage carries the entry and lander vehicles to Mars and is jettisoned prior to entry. The entry vehicle, including aeroshell, parachute and deceleration rockets, protects the lander during the direct entry and reduces its velocity from 7.6 to 0 km/s in stages during the 5 min entry sequence. The lander's touchdown is softened by airbags which are retracted once stopped on the surface. The lander then uprights itself, opens up fully and begins surface operations including deploying its camera and rover. This paper overviews the system design and the results of the system integration and test activities, including the entry, descent and landing subsystem elements. System test experiences including science instruments, the microrover, Sojourner, and software are discussed. The final qualification of the entry, descent and landing subsystems during this period is also discussed.

A new era of semiconductor genetics using ion-sensitive field-effect transistors: the gene-sensitive integrated cell.

PubMed

Toumazou, Christofer; Thay, Tan Sri Lim Kok; Georgiou, Pantelis

2014-03-28

Semiconductor genetics is now disrupting the field of healthcare owing to the rapid parallelization and scaling of DNA sensing using ion-sensitive field-effect transistors (ISFETs) fabricated using commercial complementary metal -oxide semiconductor technology. The enabling concept of DNA reaction monitoring introduced by Toumazou has made this a reality and we are now seeing relentless scaling with Moore's law ultimately achieving the $100 genome. In this paper, we present the next evolution of this technology through the creation of the gene-sensitive integrated cell (GSIC) for label-free real-time analysis based on ISFETs. This device is derived from the traditional metal-oxide semiconductor field-effect transistor (MOSFET) and has electrical performance identical to that of a MOSFET in a standard semiconductor process, yet is capable of incorporating DNA reaction chemistries for applications in single nucleotide polymorphism microarrays and DNA sequencing. Just as application-specific integrated circuits, which are developed in much the same way, have shaped our consumer electronics industry and modern communications and memory technology, so, too, do GSICs based on a single underlying technology principle have the capacity to transform the life science and healthcare industries.

The Effect of Integrated Learning Model and Critical Thinking Skill of Science Learning Outcomes

NASA Astrophysics Data System (ADS)

Fazriyah, N.; Supriyati, Y.; Rahayu, W.

2017-02-01

This study aimed to determine the effect of integrated learning model and critical thinking skill toward science learning outcomes. The study was conducted in SDN Kemiri Muka 1 Depok in fifth grade school year 2014/2015 using cluster random sampling was done to 80 students. Retrieval of data obtained through tests and analysis by Variance (ANOVA) and two lines with the design treatment by level 2x2. The results showed that: (1) science learning outcomes students that given thematic integrated learning model is higher than in the group of students given fragmented learning model, (2) there is an interaction effect between critical thinking skills with integrated learning model, (3) for students who have high critical thinking skills, science learning outcomes students who given by thematic integrated learning model higher than fragmented learning model and (4) for students who have the ability to think critically low yield higher learning science fragmented model. The results of this study indicate that thematic learning model with critical thinking skills can improve science learning outcomes of students.

Integrating Climate and Risk-Informed Science to Support Critical Decisions

ScienceCinema

None

2018-01-16

The PNNL Environmental Health and Remediation Sector stewards several decision support capabilities to integrate climate- and risk-informed science to support critical decisions. Utilizing our expertise in risk and decision analysis, integrated Earth systems modeling, and remote sensing and geoinformatics, PNNL is influencing the way science informs high level decisions at national, regional and local scales to protect and preserve our most critical assets.

Integrating Climate and Risk-Informed Science to Support Critical Decisions

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

None

2016-07-27

The PNNL Environmental Health and Remediation Sector stewards several decision support capabilities to integrate climate- and risk-informed science to support critical decisions. Utilizing our expertise in risk and decision analysis, integrated Earth systems modeling, and remote sensing and geoinformatics, PNNL is influencing the way science informs high level decisions at national, regional and local scales to protect and preserve our most critical assets.

How research funding agencies support science integration into policy and practice: An international overview

PubMed Central

2014-01-01

Background Funding agencies constitute one essential pillar for policy makers, researchers and health service delivery institutions. Such agencies are increasingly providing support for science implementation. In this paper, we investigate health research funding agencies and how they support the integration of science into policy, and of science into practice, and vice versa. Methods We selected six countries: Australia, The Netherlands, France, Canada, England and the United States. For 13 funding agencies, we compared their intentions to support, their actions related to science integration into policy and practice, and the reported benefits of this integration. We did a qualitative content analysis of the reports and information provided on the funding agencies’ websites. Results Most funding agencies emphasized the importance of science integration into policy and practice in their strategic orientation, and stated how this integration was structured. Their funding activities were embedded in the push, pull, or linkage/exchange knowledge transfer model. However, few program funding efforts were based on all three models. The agencies reported more often on the benefits of integration on practice, rather than on policy. External programs that were funded largely covered science integration into policy and practice at the end of grant stage, while overlooking the initial stages. Finally, external funding actions were more prominent than internally initiated bridging activities and training activities on such integration. Conclusions This paper contributes to research on science implementation because it goes beyond the two community model of researchers versus end users, to include funding agencies. Users of knowledge may be end users in health organizations like hospitals; civil servants assigned to decision making positions within funding agencies; civil servants outside of the Ministry of Health, such as the Ministry of the Environment; politicians deciding on health-related legislation; or even university researchers whose work builds on previous research. This heterogeneous sample of users may require different user-specific mechanisms for research initiation, development and dissemination. This paper builds the foundation for further discussion on science implementation from the perspective of funding agencies in the health field. In general, case studies can help in identifying best practices for evidence-informed decision making. PMID:24565209

How research funding agencies support science integration into policy and practice: an international overview.

PubMed

Smits, Pernelle A; Denis, Jean-Louis

2014-02-24

Funding agencies constitute one essential pillar for policy makers, researchers and health service delivery institutions. Such agencies are increasingly providing support for science implementation. In this paper, we investigate health research funding agencies and how they support the integration of science into policy, and of science into practice, and vice versa. We selected six countries: Australia, The Netherlands, France, Canada, England and the United States. For 13 funding agencies, we compared their intentions to support, their actions related to science integration into policy and practice, and the reported benefits of this integration. We did a qualitative content analysis of the reports and information provided on the funding agencies' websites. Most funding agencies emphasized the importance of science integration into policy and practice in their strategic orientation, and stated how this integration was structured. Their funding activities were embedded in the push, pull, or linkage/exchange knowledge transfer model. However, few program funding efforts were based on all three models. The agencies reported more often on the benefits of integration on practice, rather than on policy. External programs that were funded largely covered science integration into policy and practice at the end of grant stage, while overlooking the initial stages. Finally, external funding actions were more prominent than internally initiated bridging activities and training activities on such integration. This paper contributes to research on science implementation because it goes beyond the two community model of researchers versus end users, to include funding agencies. Users of knowledge may be end users in health organizations like hospitals; civil servants assigned to decision making positions within funding agencies; civil servants outside of the Ministry of Health, such as the Ministry of the Environment; politicians deciding on health-related legislation; or even university researchers whose work builds on previous research. This heterogeneous sample of users may require different user-specific mechanisms for research initiation, development and dissemination. This paper builds the foundation for further discussion on science implementation from the perspective of funding agencies in the health field. In general, case studies can help in identifying best practices for evidence-informed decision making.

Mind the gap; seven reasons to close fragmented genome assemblies

USDA-ARS?s Scientific Manuscript database

Like other domains of life, research into the biology of filamentous microbes has greatly benefited from the advent of whole-genome sequencing. Next-generation sequencing (NGS) technologies have revolutionized sequencing, making genomic sciences accessible to many academic laboratories including tho...

The effectiveness of an integrated conceptual approach to teaching middle school science: A mixed methods investigation

NASA Astrophysics Data System (ADS)

Frampton, Susan K.

This study was designed to compare the effectiveness of using traditional and integrated instructional strategies to increase student understanding of the core concepts of energy. There are mixed messages in the literature as to the success of using an integrated approach to teach science content, despite suggestions its use improves student achievement and attitudes toward science. This study used a mixed-method approach. The quantitative portion was a quasi-experimental non-equivalent control group design, and the qualitative portion included teacher journals, teacher interviews and student journals. There were three teacher participants, two in the treatment group from a district in Sussex County, Delaware. The third teacher participant, from a different district in Sussex County, Delaware was in the control group. The treatment group consisted of 180 students and the control group consisted of 124 students. The results of this study show that the treatment group had significantly less anxiety in science following the treatment, than students in the control group. The F value of 10.89 was significant at p = 0.001. Students in the treatment group also had more enjoyment of and motivation in science than did students in the control group. The F value of 25.025 was significant at a p = 0.000 for the subscale enjoyment of science. The F value of 14.1 was significant at a p = 0.000 for the subscale of motivation in science. Students in the treatment group performed significantly better on the achievement tests, the Integrated Summative Energy Assessment (ISEA) and the science portion of the Delaware State Testing Program (DSTP). The treatment group performed significantly better on the ISEA than did the control group, with an F value of 407.7 significant at p = 0.000. The treatment group performed significantly better on the science DSTP than the control group, with an F value of 65.81 which was significant at p = 0.000. The use of an integrated approach to science instruction decreases student anxiety, increases enjoyment of science and motivation in science more than a traditional approach to teaching science. The use of an integrated approach to science instruction increases student achievement on extended response assessments that measure integrated conceptual knowledge and increases student achievement on traditional summative assessments.

Key steps for integrating a basic science throughout a medical school curriculum using an e-learning approach.

PubMed

Dubois, Eline Agnès; Franson, Kari Lanette

2009-09-01

Basic sciences can be integrated into the medical school curriculum via e-learning. The process of integrating a basic science in this manner resembles a curricular change. The change usually begins with an idea for using e-learning to teach a basic science and establishing the need for the innovation. In the planning phase, learning outcomes are formulated and a prototype of the program is developed based on the desired requirements. A realistic concept is formed after considering the limitations of the current institute. Next, a project team is assembled to develop the program and plan its integration. Incorporation of the e-learning program is facilitated by a well-developed and communicated integration plan. Various course coordinators are contacted to determine content of the e-learning program as well as establish assessment. Linking the e-learning program to existing course activities and thereby applying the basic science into the clinical context enhances the degree of integration. The success of the integration is demonstrated by a positive assessment of the program including favourable cost-benefit analysis and improved student performance. Lastly, when the program becomes institutionalised, continuously updating content and technology (when appropriate), and evaluating the integration contribute to the prolonged survival of the e-learning program.

The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis

PubMed Central

Rampp, Markus; Soddemann, Thomas; Lederer, Hermann

2006-01-01

We describe a versatile and extensible integrated bioinformatics toolkit for the analysis of biological sequences over the Internet. The web portal offers convenient interactive access to a growing pool of chainable bioinformatics software tools and databases that are centrally installed and maintained by the RZG. Currently, supported tasks comprise sequence similarity searches in public or user-supplied databases, computation and validation of multiple sequence alignments, phylogenetic analysis and protein–structure prediction. Individual tools can be seamlessly chained into pipelines allowing the user to conveniently process complex workflows without the necessity to take care of any format conversions or tedious parsing of intermediate results. The toolkit is part of the Max-Planck Integrated Gene Analysis System (MIGenAS) of the Max Planck Society available at (click ‘Start Toolkit’). PMID:16844980

Common fragile sites (CFS) and extremely large CFS genes are targets for human papillomavirus integrations and chromosome rearrangements in oropharyngeal squamous cell carcinoma.

PubMed

Gao, Ge; Johnson, Sarah H; Vasmatzis, George; Pauley, Christina E; Tombers, Nicole M; Kasperbauer, Jan L; Smith, David I

2017-01-01

Common fragile sites (CFS) are chromosome regions that are prone to form gaps or breaks in response to DNA replication stress. They are often found as hotspots for sister chromatid exchanges, deletions, and amplifications in different cancers. Many of the CFS regions are found to span genes whose genomic sequence is greater than 1 Mb, some of which have been demonstrated to function as important tumor suppressors. CFS regions are also hotspots for human papillomavirus (HPV) integrations in cervical cancer. We used mate-pair sequencing to examine HPV integration events and chromosomal structural variations in 34 oropharyngeal squamous cell carcinoma (OPSCC). We used endpoint PCR and Sanger sequencing to validate each HPV integration event and found HPV integrations preferentially occurred within CFS regions similar to what is observed in cervical cancer. We also found that many of the chromosomal alterations detected also occurred at or near the cytogenetic location of CFSs. Several large genes were also found to be recurrent targets of rearrangements, independent of HPV integrations, including CSMD1 (2.1Mb), LRP1B (1.9Mb), and LARGE1 (0.7Mb). Sanger sequencing revealed that the nucleotide sequences near to identified junction sites contained repetitive and AT-rich sequences that were shown to have the potential to form stem-loop DNA secondary structures that might stall DNA replication fork progression during replication stress. This could then cause increased instability in these regions which could lead to cancer development in human cells. Our findings suggest that CFSs and some specific large genes appear to play important roles in OPSCC. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Pacific Elementary Science: A Case Study of Educational Planning for Small Developing Nations.

ERIC Educational Resources Information Center

Taylor, Neil; Vlaardingerbroek, Barand

2000-01-01

Evaluates Science Education in Pacific Schools (SEPS), a project addressing science-education deficiencies in 12 small Pacific Island countries. The assessment revealed inadequate, outdated, and unattractive science teaching resources in some countries; badly sequenced and duplicative curriculum projects across the region; and lack of teacher…

Great Explorations in Math and Science[R] (GEMS[R]) Space Science. What Works Clearinghouse Intervention Report

ERIC Educational Resources Information Center

What Works Clearinghouse, 2012

2012-01-01

"Great Explorations in Math and Science[R] (GEMS[R]) Space Science" is an instructional sequence for grades 3-5 that covers fundamental concepts, including planetary sizes and distance, the Earth's shape and movement, gravity, and moon phases and eclipses. Part of the "GEMS"[R] core curriculum, "GEMS[R] Space Science"…

Investigating Human Impact in the Environment with Faded Scaffolded Inquiry Supported by Technologies

ERIC Educational Resources Information Center

Campbell, Todd; Longhurst, Max; Duffy, Aaron M.; Wolf, Paul G.; Nagy, Robin

2012-01-01

Teaching science as inquiry is advocated in all national science education documents and by leading science and science teaching organizations. In addition to teaching science as inquiry, we recognize that learning experiences need to connect to students' lives. This article details how we use a sequence of faded scaffolded inquiry supported by…

Mapping and sequencing the human genome: Science, ethics, and public policy. Final report

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

McInerney, J.D.

1993-03-31

Development of Mapping and Sequencing the Human Genome: Science, Ethics, and Public Policy followed the standard process of curriculum development at the Biological Sciences Curriculum Study (BSCS), the process is described. The production of this module was a collaborative effort between BSCS and the American Medical Association (AMA). Appendix A contains a copy of the module. Copies of reports sent to the Department of Energy (DOE) during the development process are contained in Appendix B; all reports should be on file at DOE. Appendix B also contains copies of status reports submitted to the BSCS Board of Directors.

Exploring the value and role of integrated supportive science courses in the reformed medical curriculum iMED: a mixed methods study.

PubMed

Eisenbarth, Sophie; Tilling, Thomas; Lueerss, Eva; Meyer, Jelka; Sehner, Susanne; Guse, Andreas H; Guse Nee Kurré, Jennifer

2016-04-29

Heterogeneous basic science knowledge of medical students is an important challenge for medical education. In this study, the authors aimed at exploring the value and role of integrated supportive science (ISS) courses as a novel approach to address this challenge and to promote learning basic science concepts in medical education. ISS courses were embedded in a reformed medical curriculum. The authors used a mixed methods approach including four focus groups involving ISS course lecturers and students (two each), and five surveys of one student cohort covering the results of regular student evaluations including the ISS courses across one study year. They conducted their study at the University Medical Center Hamburg-Eppendorf between December 2013 and July 2014. Fourteen first-year medical students and thirteen ISS course lecturers participated in the focus groups. The authors identified several themes focused on the temporal integration of ISS courses into the medical curriculum, the integration of ISS course contents into core curriculum contents, the value and role of ISS courses, and the courses' setting and atmosphere. The integrated course concept was positively accepted by both groups, with participants suggesting that it promotes retention of basic science knowledge. Values and roles identified by focus group participants included promotion of basic understanding of science concepts, integration of foundational and applied learning, and maximization of students' engagement and motivation. Building close links between ISS course contents and the core curriculum appeared to be crucial. Survey results confirmed qualitative findings regarding students' satisfaction, with some courses still requiring optimization. Integration of supportive basic science courses, traditionally rather part of premedical education, into the medical curriculum appears to be a feasible strategy to improve medical students' understanding of basic science concepts and to increase their motivation and engagement.

Pros and cons of vertical integration between clinical medicine and basic science within a problem-based undergraduate medical curriculum: examples and experiences from Linköping, Sweden.

PubMed

Dahle, L O; Brynhildsen, J; Behrbohm Fallsberg, M; Rundquist, I; Hammar, M

2002-05-01

Problem-based learning (PBL), combined with early patient contact, multiprofessional education and emphasis on development of communications skills, has become the basis for the medical curriculum at the Faculty of Health Sciences in Linköping (FHS), Sweden, which was started in 1986. Important elements in the curriculum are vertical integration, i.e. integration between the clinical and basic science parts of the curriculum and horizontal integration between different subject areas. This article discusses the importance of vertical integration in an undergraduate medical curriculum, according to experiences from the Faculty of Health Sciences in Linköping, and also give examples on how it has been implemented during the latest 15 years. Results and views put forward in published articles concerning vertical integration within undergraduate medical education are discussed in relation to the experiences in Linköping. Vertical integration between basic sciences and clinical medicine in a PBL setting has been found to stimulate profound rather than superficial learning, and thereby stimulates better understanding of important biomedical principles. Integration probably leads to better retention of knowledge and the ability to apply basic science principles in the appropriate clinical context. Integration throughout the whole curriculum entails a lot of time and work in respect of planning, organization and execution. The teachers have to be deeply involved and enthusiastic and have to cooperate over departmental borders, which may produce positive spin-off effects in teaching and research but also conflicts that have to be resolved. The authors believe vertical integration supports PBL and stimulates deep and lifelong learning.

EMC Testing on the Integrated Science Instrument Module (ISIM) - A Summary of the EMC Test Campaign for the Science Payload of the James Webb Space Telescope (JWST)

NASA Technical Reports Server (NTRS)

McCloskey, John

2016-01-01

This paper describes the electromagnetic compatibility (EMC) tests performed on the Integrated Science Instrument Module (ISIM), the science payload of the James Webb Space Telescope (JWST), at NASAs Goddard Space Flight Center (GSFC) in August 2015. By its very nature of being an integrated payload, it could be treated as neither a unit level test nor an integrated spacecraft/observatory test. Non-standard test criteria are described along with non-standard test methods that had to be developed in order to evaluate them. Results are presented to demonstrate that all test criteria were met in less than the time allocated.

Biological data sciences in genome research.

PubMed

Schatz, Michael C

2015-10-01

The last 20 years have been a remarkable era for biology and medicine. One of the most significant achievements has been the sequencing of the first human genomes, which has laid the foundation for profound insights into human genetics, the intricacies of regulation and development, and the forces of evolution. Incredibly, as we look into the future over the next 20 years, we see the very real potential for sequencing more than 1 billion genomes, bringing even deeper insight into human genetics as well as the genetics of millions of other species on the planet. Realizing this great potential for medicine and biology, though, will only be achieved through the integration and development of highly scalable computational and quantitative approaches that can keep pace with the rapid improvements to biotechnology. In this perspective, I aim to chart out these future technologies, anticipate the major themes of research, and call out the challenges ahead. One of the largest shifts will be in the training used to prepare the class of 2035 for their highly interdisciplinary world. © 2015 Schatz; Published by Cold Spring Harbor Laboratory Press.

Impact of Integrated Science and English Language Arts Literacy Supplemental Instructional Intervention on Science Academic Achievement of Elementary Students

ERIC Educational Resources Information Center

Marks, Jamar Terry

2017-01-01

The purpose of this quasi-experimental, nonequivalent pretest-posttest control group design study was to determine if any differences existed in upper elementary school students' science academic achievement when instructed using an 8-week integrated science and English language arts literacy supplemental instructional intervention in conjunction…

Examining the Conceptual Organization of Students in an Integrated Algebra and Physical Science Class.

ERIC Educational Resources Information Center

Westbrook, Susan L.

1998-01-01

Compares the conceptual organization of students in an integrated algebra and physical science class (SAM 9) with that of students in a discipline-specific physical science class (PSO). Analysis of students' concept maps indicates that the SAM9 students used a greater number of procedural linkages to connect mathematics and science concepts than…

the Integrated Science Textbooks in China

ERIC Educational Resources Information Center

Wei, Bing; Li, Yue; Chen, Bo

2013-01-01

This study aimed to examine the representations of nature of science (NOS) in the eight histories of science selected from three series of integrated science textbooks used in junior high school in China. Ten aspects of NOS were adopted in the analytical framework. It was found that NOS had not been well treated in the selected histories of…

Challenges and Support When Teaching Science through an Integrated Inquiry and Literacy Approach

ERIC Educational Resources Information Center

Ødegaard, Marianne; Haug, Berit; Mork, Sonja M.; Sørvik, Gard Ove

2014-01-01

In the Budding Science and Literacy project, we explored how working with an integrated inquiry-based science and literacy approach may challenge and support the teaching and learning of science at the classroom level. By studying the inter-relationship between multiple learning modalities and phases of inquiry, we wished to illuminate possible…

The Impact of Design-Based STEM Integration Curricula on Student Achievement in Engineering, Science, and Mathematics

ERIC Educational Resources Information Center

Selcen Guzey, S.; Harwell, Michael; Moreno, Mario; Peralta, Yadira; Moore, Tamara J.

2017-01-01

The new science education reform documents call for integration of engineering into K-12 science classes. Engineering design and practices are new to most science teachers, meaning that implementing effective engineering instruction is likely to be challenging. This quasi-experimental study explored the influence of teacher-developed, engineering…

Identifying and Verifying Earthquake Engineering Concepts to Create a Knowledge Base in STEM Education: A Modified Delphi Study

ERIC Educational Resources Information Center

Cavlazoglu, Baki; Stuessy, Carol L.

2017-01-01

Stakeholders in STEM education have called for integrating engineering content knowledge into STEM-content classrooms. To answer the call, stakeholders in science education announced a new framework, Next Generation Science Standards, which focuses on the integration of science and engineering in K-12 science education. However, research indicates…

Integrating History of Science in Science Education through Historical Microworlds to Promote Conceptual Change

ERIC Educational Resources Information Center

Masson, Steve; Vazquez-Abad, Jesus

2006-01-01

This paper proposes a new way to integrate history of science in science education to promote conceptual change by introducing the notion of historical microworld, which is a computer-based interactive learning environment respecting historic conceptions. In this definition, "interactive" means that the user can act upon the virtual environment by…

Science as the Center of a Coherent, Integrated Early Childhood Curriculum

ERIC Educational Resources Information Center

French, Lucia

2004-01-01

This article describes the ScienceStart! Curriculum, an early childhood curriculum that takes coherently organized science content as the hub of an integrated approach. ScienceStart! maps onto the typical preschool day and may be adapted for use in full-day or half-day preschool programs. It is designed to support the important developmental…

An Innovative Course Featuring Action Research Integrated with Unifying Science Themes

ERIC Educational Resources Information Center

Otto, Charlotte A.; Luera, Gail R.; Everett, Susan A.

2009-01-01

In this article, we describe an innovative capstone course for preservice K-8 teachers integrating action research and a unifying theme in science (AAAS in Science for all Americans. Oxford University Press, New York, 1989; NRC in National science education standards. National Academy Press, Washington, DC, 1996). The goals of the capstone course…

USE OF THE SDO POINTING CONTROLLERS FOR INSTRUMENT CALIBRATION MANEUVERS

NASA Technical Reports Server (NTRS)

Vess, Melissa F.; Starin, Scott R.; Morgenstern, Wendy M.

2005-01-01

During the science phase of the Solar Dynamics Observatory mission, the three science instruments require periodic instrument calibration maneuvers with a frequency of up to once per month. The command sequences for these maneuvers vary in length from a handful of steps to over 200 steps, and individual steps vary in size from 5 arcsec per step to 22.5 degrees per step. Early in the calibration maneuver development, it was determined that the original attitude sensor complement could not meet the knowledge requirements for the instrument calibration maneuvers in the event of a sensor failure. Because the mission must be single fault tolerant, an attitude determination trade study was undertaken to determine the impact of adding an additional attitude sensor versus developing alternative, potentially complex, methods of performing the maneuvers in the event of a sensor failure. To limit the impact to the science data capture budget, these instrument calibration maneuvers must be performed as quickly as possible while maintaining the tight pointing and knowledge required to obtain valid data during the calibration. To this end, the decision was made to adapt a linear pointing controller by adjusting gains and adding an attitude limiter so that it would be able to slew quickly and still achieve steady pointing once on target. During the analysis of this controller, questions arose about the stability of the controller during slewing maneuvers due to the combination of the integral gain, attitude limit, and actuator saturation. Analysis was performed and a method for disabling the integral action while slewing was incorporated to ensure stability. A high fidelity simulation is used to simulate the various instrument calibration maneuvers.

The Effect of a Literature-Based Program Integrated into Literacy and Science Instruction on Achievement, Use, and Attitudes toward Literacy and Science. Reading Research Report No. 37.

ERIC Educational Resources Information Center

Morrow, Lesley Mandel; And Others

A study determined the impact of integrating literacy and science programs on literacy achievement, use of literature, and attitude toward reading and science. Six third-grade classes (128 students) of ethnically diverse children were assigned to one control and two experimental groups (literature/science program and literature only program).…

[Problems of world outlook and methodology of science integration in biological studies].

PubMed

Khododova, Iu D

1981-01-01

Problems of worldoutlook and methodology of the natural-science knowledge are considered basing on the analysis of tendencies in the development of the membrane theory of cell processes and the use of principles of biological membrane functioning when solving some scientific and applied problems pertaining to different branches of chemistry and biology. The notion scientific knowledge integration is defined as interpenetration of approaches, methods and ideas of different branches of knowledge and enrichment on this basis of their content resulting in knowledge augmentation in each field taken separately. These processes are accompanied by appearance of new branches of knowledge - sciences "on junction" and their subsequent differentiations. The analysis of some gnoseological situations shows that integration of sciences contributes to coordination and some agreement of thinking styles of different specialists, puts forward keen personality of a scientist demanding, in particular, his high professional mobility. Problems of scientific activity organization are considered, which involve social sciences into the integration processes. The role of philosophy in the integration processes is emphasized.

Application of Model Project Based Learning on Integrated Science in Water Pollution

NASA Astrophysics Data System (ADS)

Yamin, Y.; Permanasari, A.; Redjeki, S.; Sopandi, W.

2017-09-01

The function of this research was to analyze the influence model Project Based Learning (PjBl) on integrated science about the concept mastery for junior high school students. Method used for this research constitutes the quasi of experiment method. Population and sample for this research are the students junior high school in Bandung as many as two classes to be experiment and control class. The instrument that used for this research is the test concept mastery, assessment questionnaire of product and the questionnaire responses of the student about learning integrated science. Based on the result of this research get some data that with accomplishment the model of PjBl. Learning authority of integrated science can increase the concept mastery for junior high school students. The highest increase in the theme of pollution water is in the concept of mixtures and the separation method. The students give a positive response in learning of integrated science for the theme of pollution of the water used model PjBL with questionnaire of the opinion aspect in amount of 83.5%, the anxiety of the students in amount of 95.5%, the profit learning model of PjBL in amount of 96.25% and profit learning of integrated science in amount of 95.75%.

Pioneering University/Industry Venture Explores VLSI Frontiers.

ERIC Educational Resources Information Center

Davis, Dwight B.

1983-01-01

Discusses industry-sponsored programs in semiconductor research, focusing on Stanford University's Center for Integrated Systems (CIS). CIS, while pursuing research in semiconductor very-large-scale integration, is merging the fields of computer science, information science, and physical science. Issues related to these university/industry…

76 FR 370 - Center for Scientific Review; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-04

... . Name of Committee: Genes, Genomes, and Genetics Integrated Review Group; Molecular Genetics B Study... Committee: Cardiovascular and Respiratory Sciences Integrated Review Group; Lung Cellular, Molecular, and... Committee: Population Sciences and Epidemiology Integrated Review Group; Behavioral Genetics and...

Characterization of genetic elements required for site-specific integration of Lactobacillus delbrueckii subsp. bulgaricus bacteriophage mv4 and construction of an integration-proficient vector for Lactobacillus plantarum.

PubMed Central

Dupont, L; Boizet-Bonhoure, B; Coddeville, M; Auvray, F; Ritzenthaler, P

1995-01-01

Temperate phage mv4 integrates its DNA into the chromosome of Lactobacillus delbrueckii subsp. bulgaricus strains via site-specific recombination. Nucleotide sequencing of a 2.2-kb attP-containing phage fragment revealed the presence of four open reading frames. The larger open reading frame, close to the attP site, encoded a 427-amino-acid polypeptide with similarity in its C-terminal domain to site-specific recombinases of the integrase family. Comparison of the sequences of attP, bacterial attachment site attB, and host-phage junctions attL and attR identified a 17-bp common core sequence, where strand exchange occurs during recombination. Analysis of the attB sequence indicated that the core region overlaps the 3' end of a tRNA(Ser) gene. Phage mv4 DNA integration into the tRNA(Ser) gene preserved an intact tRNA(Ser) gene at the attL site. An integration vector based on the mv4 attP site and int gene was constructed. This vector transforms a heterologous host, L. plantarum, through site-specific integration into the tRNA(Ser) gene of the genome and will be useful for development of an efficient integration system for a number of additional bacterial species in which an identical tRNA gene is present. PMID:7836291

Integrating Science Content and Pedagogy in the Earth, Life, and Physical Sciences: A K-8 Pre-Service Teacher Preparation Continuum at the University of Delaware

NASA Astrophysics Data System (ADS)

Madsen, J.; Allen, D.; Donham, R.; Fifield, S.; Ford, D.; Shipman, H.; Dagher, Z.

2007-12-01

University of Delaware faculty in the geological sciences, biological sciences, and the physics and astronomy departments have partnered with faculty and researchers from the school of education to form a continuum for K- 8 pre-service teacher preparation in science. The goal of the continuum is to develop integrated understandings of content and pedagogy so that these future teachers can effectively use inquiry-based approaches in teaching science in their classrooms. Throughout the continuum where earth science content appears an earth system science approach, with emphasis on inquiry-based activities, is employed. The continuum for K-8 pre-service teachers includes a gateway content course in the earth, life, or physical sciences taken during the freshman year followed by integrated science content and methods courses taken during the sophomore year. These integrated courses, called the Science Semester, were designed and implemented with funding from the National Science Foundation. During the Science Semester, traditional content and pedagogy subject matter boundaries are crossed to stress shared themes that teachers must understand to teach standards-based science. Students work collaboratively on multidisciplinary problem-based learning (PBL) activities that place science concepts in authentic contexts and build learning skills. They also critically explore the theory and practice of elementary science teaching, drawing on their shared experiences of inquiry learning during the Science Semester. The PBL activities that are the hallmark of the Science Semester provide the backdrop through which fundamental earth system interactions can be studied. For example in a PBL investigation that focuses on kids, cancer, and the environment, the hydrologic cycle with emphasis on surface runoff and ground water contamination is studied. Those students seeking secondary certification in science will enroll, as a bridge toward their student teaching experience, in an additional content course within a science discipline that is concurrently taught with a science methods course. Emphasizing inquiry-based activities, these bridge courses also focus on developing integrated understandings of the sciences. The continuum extends beyond the student teaching experience by tracking cohorts of science teachers during their in-service years. With funding from the National Science Foundation's Teacher Professional Continuum program, we are conducting research on this inquiry-based professional development approach for K-8 teachers across this continuum.

Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow.

PubMed

Suryawanshi, Gajendra W; Xu, Song; Xie, Yiming; Chou, Tom; Kim, Namshin; Chen, Irvin S Y; Kim, Sanggu

2017-06-14

Integration Site (IS) assays are a critical component of the study of retroviral integration sites and their biological significance. In recent retroviral gene therapy studies, IS assays, in combination with next-generation sequencing, have been used as a cell-tracking tool to characterize clonal stem cell populations sharing the same IS. For the accurate comparison of repopulating stem cell clones within and across different samples, the detection sensitivity, data reproducibility, and high-throughput capacity of the assay are among the most important assay qualities. This work provides a detailed protocol and data analysis workflow for bidirectional IS analysis. The bidirectional assay can simultaneously sequence both upstream and downstream vector-host junctions. Compared to conventional unidirectional IS sequencing approaches, the bidirectional approach significantly improves IS detection rates and the characterization of integration events at both ends of the target DNA. The data analysis pipeline described here accurately identifies and enumerates identical IS sequences through multiple steps of comparison that map IS sequences onto the reference genome and determine sequencing errors. Using an optimized assay procedure, we have recently published the detailed repopulation patterns of thousands of Hematopoietic Stem Cell (HSC) clones following transplant in rhesus macaques, demonstrating for the first time the precise time point of HSC repopulation and the functional heterogeneity of HSCs in the primate system. The following protocol describes the step-by-step experimental procedure and data analysis workflow that accurately identifies and quantifies identical IS sequences.

Impact of Interdisciplinary Undergraduate Research in Mathematics and Biology on the Development of a New Course Integrating Five STEM Disciplines

PubMed Central

Caudill, Lester; Hill, April; Lipan, Ovidiu

2010-01-01

Funded by innovative programs at the National Science Foundation and the Howard Hughes Medical Institute, University of Richmond faculty in biology, chemistry, mathematics, physics, and computer science teamed up to offer first- and second-year students the opportunity to contribute to vibrant, interdisciplinary research projects. The result was not only good science but also good science that motivated and informed course development. Here, we describe four recent undergraduate research projects involving students and faculty in biology, physics, mathematics, and computer science and how each contributed in significant ways to the conception and implementation of our new Integrated Quantitative Science course, a course for first-year students that integrates the material in the first course of the major in each of biology, chemistry, mathematics, computer science, and physics. PMID:20810953

Impact of Interdisciplinary Undergraduate Research in mathematics and biology on the development of a new course integrating five STEM disciplines.

PubMed

Caudill, Lester; Hill, April; Hoke, Kathy; Lipan, Ovidiu

2010-01-01

Funded by innovative programs at the National Science Foundation and the Howard Hughes Medical Institute, University of Richmond faculty in biology, chemistry, mathematics, physics, and computer science teamed up to offer first- and second-year students the opportunity to contribute to vibrant, interdisciplinary research projects. The result was not only good science but also good science that motivated and informed course development. Here, we describe four recent undergraduate research projects involving students and faculty in biology, physics, mathematics, and computer science and how each contributed in significant ways to the conception and implementation of our new Integrated Quantitative Science course, a course for first-year students that integrates the material in the first course of the major in each of biology, chemistry, mathematics, computer science, and physics.

Integrated translational genomics for analysis of complex traits in sorghum

USDA-ARS?s Scientific Manuscript database

We will report on the integration of sequencing and genotype data from natural variation (by whole genome resequencing [wgs] or genotype by sequencing [gbs]), transcriptome (RNA-seq) and mutant analysis (also by wgs) with the goal of identifying genes controlling important agronomic traits and tran...

An overview of the model integration process: From pre ...

EPA Pesticide Factsheets

Integration of models requires linking models which can be developed using different tools, methodologies, and assumptions. We performed a literature review with the aim of improving our understanding of model integration process, and also presenting better strategies for building integrated modeling systems. We identified five different phases to characterize integration process: pre-integration assessment, preparation of models for integration, orchestration of models during simulation, data interoperability, and testing. Commonly, there is little reuse of existing frameworks beyond the development teams and not much sharing of science components across frameworks. We believe this must change to enable researchers and assessors to form complex workflows that leverage the current environmental science available. In this paper, we characterize the model integration process and compare integration practices of different groups. We highlight key strategies, features, standards, and practices that can be employed by developers to increase reuse and interoperability of science software components and systems. The paper provides a review of the literature regarding techniques and methods employed by various modeling system developers to facilitate science software interoperability. The intent of the paper is to illustrate the wide variation in methods and the limiting effect the variation has on inter-framework reuse and interoperability. A series of recommendation

The effects of integrated mathematics/science curriculum and instruction on mathematics achievement and student attitudes in grade six

NASA Astrophysics Data System (ADS)

Hill, Mary Denise

The purpose of this study was to determine whether integrating mathematics and science curriculum and teaching practices significantly improves achievement in mathematics and attitudes towards mathematics among sixth grade students in South Texas. The study was conducted during the 2001--2002 school year. A causal-comparative ex post facto research design was used to explore the effects of integrated mathematics and science classrooms compared to classrooms of traditional, isolated mathematics and science teaching practices on student achievement and student attitudes. Achievement was based on the Spring 2002 Mathematics portion of the standardized Texas Assessment of Academic Skills (TAAS) Texas Learning Index (TLI) scores and individual student's mathematics Grade Point Average (GPA). Measurement of student attitudes was based on the results of the Integrated Mathematics Attitudinal Survey (IMAS), created by the researcher for this study. The sample population included 349 Grade 6 mathematics students attending one middle school involved in a pilot program utilizing integrated mathematics/science curriculum and teaching practices in a South Texas urban school district. The research involved 337 of the 349 sixth grade students to study the effects of mathematics/science curriculum and teaching practices on achievement and 207 of the 349 sixth grade students to study the effects of mathematics/science curriculum on attitudes concerning mathematics. The data were analyzed using chi square analyses, independent samples t-tests, and the analysis of variance (ANOVA). Statistical significance was determined at the .05 level of significance. Significant relationships were found when analyzing the proficiency of mathematics skills and individual growth of mathematics achievement. Chi square analyses indicated that the students in the integrated mathematics/science classrooms were more likely to exhibit individual growth and proficiency of mathematics skills based on the results of TAAS. Independent samples t-tests indicated that students in the integrated mathematics/science program scored significantly higher than the students in the traditional program in mean achievement scores and in mean growth of scores based on the results of TAAS. No significant differences were found when comparing mathematics anxiety scores between students in the integrated mathematics/science program and the traditional program. However, additional significant differences were identified when students in the integrated mathematics/science program scored higher than the students in the traditional program when analyzing the overall mean student attitude scores concerning mathematics and the mean scores of attitudinal values of mathematics in society.

E-MSD: an integrated data resource for bioinformatics

PubMed Central

Velankar, S.; McNeil, P.; Mittard-Runte, V.; Suarez, A.; Barrell, D.; Apweiler, R.; Henrick, K.

2005-01-01

The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the worldwide Protein Data Bank (wwPDB) and to work towards the integration of various bioinformatics data resources. One of the major obstacles to the improved integration of structural databases such as MSD and sequence databases like UniProt is the absence of up to date and well-maintained mapping between corresponding entries. We have worked closely with the UniProt group at the EBI to clean up the taxonomy and sequence cross-reference information in the MSD and UniProt databases. This information is vital for the reliable integration of the sequence family databases such as Pfam and Interpro with the structure-oriented databases of SCOP and CATH. This information has been made available to the eFamily group (http://www.efamily.org.uk/) and now forms the basis of the regular interchange of information between the member databases (MSD, UniProt, Pfam, Interpro, SCOP and CATH). This exchange of annotation information has enriched the structural information in the MSD database with annotation from wider sequence-oriented resources. This work was carried out under the ‘Structure Integration with Function, Taxonomy and Sequences (SIFTS)’ initiative (http://www.ebi.ac.uk/msd-srv/docs/sifts) in the MSD group. PMID:15608192

Unexpected Inheritance: Multiple Integrations of Ancient Bornavirus and Ebolavirus/Marburgvirus Sequences in Vertebrate Genomes

PubMed Central

Belyi, Vladimir A.; Levine, Arnold J.; Skalka, Anna Marie

2010-01-01

Vertebrate genomes contain numerous copies of retroviral sequences, acquired over the course of evolution. Until recently they were thought to be the only type of RNA viruses to be so represented, because integration of a DNA copy of their genome is required for their replication. In this study, an extensive sequence comparison was conducted in which 5,666 viral genes from all known non-retroviral families with single-stranded RNA genomes were matched against the germline genomes of 48 vertebrate species, to determine if such viruses could also contribute to the vertebrate genetic heritage. In 19 of the tested vertebrate species, we discovered as many as 80 high-confidence examples of genomic DNA sequences that appear to be derived, as long ago as 40 million years, from ancestral members of 4 currently circulating virus families with single strand RNA genomes. Surprisingly, almost all of the sequences are related to only two families in the Order Mononegavirales: the Bornaviruses and the Filoviruses, which cause lethal neurological disease and hemorrhagic fevers, respectively. Based on signature landmarks some, and perhaps all, of the endogenous virus-like DNA sequences appear to be LINE element-facilitated integrations derived from viral mRNAs. The integrations represent genes that encode viral nucleocapsid, RNA-dependent-RNA-polymerase, matrix and, possibly, glycoproteins. Integrations are generally limited to one or very few copies of a related viral gene per species, suggesting that once the initial germline integration was obtained (or selected), later integrations failed or provided little advantage to the host. The conservation of relatively long open reading frames for several of the endogenous sequences, the virus-like protein regions represented, and a potential correlation between their presence and a species' resistance to the diseases caused by these pathogens, are consistent with the notion that their products provide some important biological advantage to the species. In addition, the viruses could also benefit, as some resistant species (e.g. bats) may serve as natural reservoirs for their persistence and transmission. Given the stringent limitations imposed in this informatics search, the examples described here should be considered a low estimate of the number of such integration events that have persisted over evolutionary time scales. Clearly, the sources of genetic information in vertebrate genomes are much more diverse than previously suspected. PMID:20686665

Unexpected inheritance: multiple integrations of ancient bornavirus and ebolavirus/marburgvirus sequences in vertebrate genomes.

PubMed

Belyi, Vladimir A; Levine, Arnold J; Skalka, Anna Marie

2010-07-29

Vertebrate genomes contain numerous copies of retroviral sequences, acquired over the course of evolution. Until recently they were thought to be the only type of RNA viruses to be so represented, because integration of a DNA copy of their genome is required for their replication. In this study, an extensive sequence comparison was conducted in which 5,666 viral genes from all known non-retroviral families with single-stranded RNA genomes were matched against the germline genomes of 48 vertebrate species, to determine if such viruses could also contribute to the vertebrate genetic heritage. In 19 of the tested vertebrate species, we discovered as many as 80 high-confidence examples of genomic DNA sequences that appear to be derived, as long ago as 40 million years, from ancestral members of 4 currently circulating virus families with single strand RNA genomes. Surprisingly, almost all of the sequences are related to only two families in the Order Mononegavirales: the Bornaviruses and the Filoviruses, which cause lethal neurological disease and hemorrhagic fevers, respectively. Based on signature landmarks some, and perhaps all, of the endogenous virus-like DNA sequences appear to be LINE element-facilitated integrations derived from viral mRNAs. The integrations represent genes that encode viral nucleocapsid, RNA-dependent-RNA-polymerase, matrix and, possibly, glycoproteins. Integrations are generally limited to one or very few copies of a related viral gene per species, suggesting that once the initial germline integration was obtained (or selected), later integrations failed or provided little advantage to the host. The conservation of relatively long open reading frames for several of the endogenous sequences, the virus-like protein regions represented, and a potential correlation between their presence and a species' resistance to the diseases caused by these pathogens, are consistent with the notion that their products provide some important biological advantage to the species. In addition, the viruses could also benefit, as some resistant species (e.g. bats) may serve as natural reservoirs for their persistence and transmission. Given the stringent limitations imposed in this informatics search, the examples described here should be considered a low estimate of the number of such integration events that have persisted over evolutionary time scales. Clearly, the sources of genetic information in vertebrate genomes are much more diverse than previously suspected.

Integrated Science Assessment (ISA) for Lead (Final Report, Jul 2013)

EPA Science Inventory

EPA announced the availability of the final report, Integrated Science Assessment (ISA) for Lead (Pb). This document represents a concise synthesis and evaluation of the most policy-relevant science and will ultimately provide the scientific bases for EPA’s decision regard...

SCIENCE OF INTEGRATED WATERSHED MANAGEMENT: LINKING POLLUTANT CONTROL PRACTICES WITH WATER QUALITY

EPA Science Inventory

SCIENCE OF INTEGRATED WATERSHED MANAGEMENT: LINKING POLLUTANT CONTROL PRACTICES WITH WATER QUALITY M. Morrison (NRMRL), C. Nietch (NRMRL), 1. Schubauer-Berigan (NRMRL), M. Hantush (NRMRL), D. Lai (NRMRL), B. Daniel (NERL), M. Griffith (NCEA) Science Questions LTG 3. MYP Sc...

Integrating Science with Technical and Vocational Areas.

ERIC Educational Resources Information Center

Snyder, Larry; Shreckengast, Craig

This guide presents learning activities and lesson plans that integrate science with technical and vocational areas. Activities and plans are organized under broad headings such as Environmental Science and Acid Rain Research; Criminal Justice, Chemistry, and Narcotics; Children's Education and Services; Cosmetology; and Health Professions.…

Integrated Science Syllabus for Malaysia, Forms 1-111, Revised Version.

ERIC Educational Resources Information Center

Ministry of Education, Kuala Lumpur (Malaysia).

As a revised version of the Scottish Integrated Science, an outline of the Malaysian science course is presented in this volume for use as a guideline for science teaching at the secondary level. A total of 16 sections is included in three forms which are intended to be covered in three years. The topics include: lab techniques, unit systems,…

Effects of an Integrated Science and Societal Implication Intervention on Promoting Adolescents' Positive Thinking and Emotional Perceptions in Learning Science

ERIC Educational Resources Information Center

Hong, Zuway R.; Lin, Huann-Shyang; Lawrenz, Frances P.

2012-01-01

The goal of this study was to test the effectiveness of integrating science and societal implication on adolescents' positive thinking and emotional perceptions about learning science. Twenty-five eighth-grade Taiwanese adolescents (9 boys and 16 girls) volunteered to participate in a 12-week intervention and formed the experimental group.…

Impact of the Knowledge and Beliefs of Egyptian Science Teachers in Integrating a STS Based Curriculum: A Sociocultural Perspective

ERIC Educational Resources Information Center

Mansour, Nasser

2010-01-01

The failure of much curriculum innovation has been attributed to the neglect by innovators of teachers' perceptions. The purpose of this study was to investigate inservice science teachers views of integrating Science, Technology and Society (STS) issues into the science curriculum and identify the factors that influence their decisions concerning…

The Integration of HIV and AIDS as a Socio-Scientific Issue in the Life Sciences Curriculum

ERIC Educational Resources Information Center

Wolff, Eugenie; Mnguni, Lindelani

2015-01-01

The potential of science to transform lives has been highlighted by a number of scholars. This means that critical socio-scientific issues (SSIs) must be integrated into science curricula. Development of context-specific scientific knowledge and twenty-first-century learning skills in science education could be used to address SSIs such as…

Collaborations in a Community of Practice Working to Integrate Engineering Design in Elementary Science Education

ERIC Educational Resources Information Center

Lehman, James D.; Kim, WooRi; Harris, Constance

2014-01-01

The new standards for K-12 science education in the United States call for science teachers to integrate engineering concepts and practices within their science teaching in order to improve student learning. To accomplish this, teachers need appropriate instructional materials as well as the knowledge and skills to effectively use them. This mixed…

"Do Books Like These Have Authors?" New Roles for Text and New Demands on Students in Integrated Science-Literacy Instruction

ERIC Educational Resources Information Center

Sørvik, Gard Ove; Blikstad-Balas, Marte; Ødegaard, Marianne

2015-01-01

We report on research that explores students' literacy practices in six Norwegian primary school science classrooms during integrated science-literacy instruction. The study combines observational video data and interview data to examine students' encounters with and use of text, along with their views and experiences related to science and…

Evaluation of NSF's Program of Grants and Vertical Integration of Research and Education in the Mathematical Sciences (VIGRE)

ERIC Educational Resources Information Center

National Academies Press, 2009

2009-01-01

In 1998, the National Science Foundation (NSF) launched a program of Grants for Vertical Integration of Research and Education in the Mathematical Sciences (VIGRE). These grants were designed for institutions with PhD-granting departments in the mathematical sciences, for the purpose of developing high-quality education programs, at all levels,…

Clinical Competencies and the Basic Sciences: An Online Case Tutorial Paradigm for Delivery of Integrated Clinical and Basic Science Content

ERIC Educational Resources Information Center

DiLullo, Camille; Morris, Harry J.; Kriebel, Richard M.

2009-01-01

Understanding the relevance of basic science knowledge in the determination of patient assessment, diagnosis, and treatment is critical to good medical practice. One method often used to direct students in the fundamental process of integrating basic science and clinical information is problem-based learning (PBL). The faculty facilitated small…

Symposium: The Role of Biological Sciences in the Optometric Curriculum.

ERIC Educational Resources Information Center

And Others; Rapp, Jerry

1980-01-01

Papers from a symposium probing some of the curricular elements of the program in biological sciences at a school or college of optometry are provided. The overall program sequence in the biological sciences, microbiology, pharmacology, and the curriculum in the biological sciences from a clinical perspective are discussed. (Author/MLW)

A Network for Integrated Science and Mathematics Teaching and Learning. NCSTL Monograph Series, #2.

ERIC Educational Resources Information Center

Berlin, Donna F.; White, Arthur L.

This monograph presents a summary of the results of the Wingspread Conference in April, 1991 concerning the viability and future of the concept of integration of mathematics and science teaching and learning. The conference focused on three critical issues: (1) development of definitions of integration and a rationale for integrated teaching and…

Rational design of new materials using recombinant structural proteins: Current state and future challenges.

PubMed

Sutherland, Tara D; Huson, Mickey G; Rapson, Trevor D

2018-01-01

Sequence-definable polymers are seen as a prerequisite for design of future materials, with many polymer scientists regarding such polymers as the holy grail of polymer science. Recombinant proteins are sequence-defined polymers. Proteins are dictated by DNA templates and therefore the sequence of amino acids in a protein is defined, and molecular biology provides tools that allow redesign of the DNA as required. Despite this advantage, proteins are underrepresented in materials science. In this publication we investigate the advantages and limitations of using proteins as templates for rational design of new materials. Crown Copyright © 2017. Published by Elsevier Inc. All rights reserved.

A Principle for Network Science

DTIC Science & Technology

2011-02-01

we consider is the sound of splashing water from a leaky faucet . This sequence of water drops can set your teeth on edge and leads to tossing and...intermittent sequence of water drops from a leaky faucet is described by a Lévy stable distribution that is an asymptotically inverse power-law with index...universality of physics: the conservation of energy, symmetry principles, and the laws of thermodynamics have no analogs in the soft sciences. This

LLNL's Big Science Capabilities Help Spur Over $796 Billion in U.S. Economic Activity Sequencing the Human Genome

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

Stewart, Jeffrey S.

LLNL’s successful history of taking on big science projects spans beyond national security and has helped create billions of dollars per year in new economic activity. One example is LLNL’s role in helping sequence the human genome. Over $796 billion in new economic activity in over half a dozen fields has been documented since LLNL successfully completed this Grand Challenge.

Multiplex picoliter-droplet digital PCR for quantitative assessment of DNA integrity in clinical samples.

PubMed

Didelot, Audrey; Kotsopoulos, Steve K; Lupo, Audrey; Pekin, Deniz; Li, Xinyu; Atochin, Ivan; Srinivasan, Preethi; Zhong, Qun; Olson, Jeff; Link, Darren R; Laurent-Puig, Pierre; Blons, Hélène; Hutchison, J Brian; Taly, Valerie

2013-05-01

Assessment of DNA integrity and quantity remains a bottleneck for high-throughput molecular genotyping technologies, including next-generation sequencing. In particular, DNA extracted from paraffin-embedded tissues, a major potential source of tumor DNA, varies widely in quality, leading to unpredictable sequencing data. We describe a picoliter droplet-based digital PCR method that enables simultaneous detection of DNA integrity and the quantity of amplifiable DNA. Using a multiplex assay, we detected 4 different target lengths (78, 159, 197, and 550 bp). Assays were validated with human genomic DNA fragmented to sizes of 170 bp to 3000 bp. The technique was validated with DNA quantities as low as 1 ng. We evaluated 12 DNA samples extracted from paraffin-embedded lung adenocarcinoma tissues. One sample contained no amplifiable DNA. The fractions of amplifiable DNA for the 11 other samples were between 0.05% and 10.1% for 78-bp fragments and ≤1% for longer fragments. Four samples were chosen for enrichment and next-generation sequencing. The quality of the sequencing data was in agreement with the results of the DNA-integrity test. Specifically, DNA with low integrity yielded sequencing results with lower levels of coverage and uniformity and had higher levels of false-positive variants. The development of DNA-quality assays will enable researchers to downselect samples or process more DNA to achieve reliable genome sequencing with the highest possible efficiency of cost and effort, as well as minimize the waste of precious samples. © 2013 American Association for Clinical Chemistry.

SPATIALLY RESOLVED STAR FORMATION MAIN SEQUENCE OF GALAXIES IN THE CALIFA SURVEY

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

Cano-Díaz, M.; Sánchez, S. F.; Zibetti, S.

2016-04-20

The “main sequence of galaxies”–defined in terms of the total star formation rate ψ versus the total stellar mass M {sub *}—is a well-studied tight relation that has been observed at several wavelengths and at different redshifts. All earlier studies have derived this relation from integrated properties of galaxies. We recover the same relation from an analysis of spatially resolved properties, with integral field spectroscopic (IFS) observations of 306 galaxies from the CALIFA survey. We consider the SFR surface density in units of log( M {sub ⊙} yr{sup −1} Kpc{sup −2}) and the stellar mass surface density in units ofmore » log( M {sub ⊙} Kpc{sup −2}) in individual spaxels that probe spatial scales of 0.5–1.5 Kpc. This local relation exhibits a high degree of correlation with small scatter ( σ = 0.23 dex), irrespective of the dominant ionization source of the host galaxy or its integrated stellar mass. We highlight (i) the integrated star formation main sequence formed by galaxies whose dominant ionization process is related to star formation, for which we find a slope of 0.81 ± 0.02; (ii) for the spatially resolved relation obtained with the spaxel analysis, we find a slope of 0.72 ± 0.04; and (iii) for the integrated main sequence, we also identified a sequence formed by galaxies that are dominated by an old stellar population, which we have called the retired galaxies sequence.« less

Low incidence of DNA sequence variation in human induced pluripotent stem cells generated by non-integrating plasmid expression

PubMed Central

Cheng, Linzhao; Hansen, Nancy F.; Zhao, Ling; Du, Yutao; Zou, Chunlin; Donovan, Frank X.; Chou, Bin-Kuan; Zhou, Guangyu; Li, Shijie; Dowey, Sarah N.; Ye, Zhaohui; Chandrasekharappa, Settara C.; Yang, Huanming; Mullikin, James C.; Liu, P. Paul

2012-01-01

Summary The utility of induced pluripotent stem cells (iPSCs) as models to study diseases and as sources for cell therapy depends on the integrity of their genomes. Despite recent publications of DNA sequence variations in the iPSCs, the true scope of such changes for the entire genome is not clear. Here we report the whole-genome sequencing of three human iPSC lines derived from two cell types of an adult donor by episomal vectors. The vector sequence was undetectable in the deeply sequenced iPSC lines. We identified 1058–1808 heterozygous single nucleotide variants (SNVs), but no copy number variants, in each iPSC line. Six to twelve of these SNVs were within coding regions in each iPSC line, but ~50% of them are synonymous changes and the remaining are not selectively enriched for known genes associated with cancers. Our data thus suggest that episome-mediated reprogramming is not inherently mutagenic during integration-free iPSC induction. PMID:22385660

Integrating Climate Change Science and Sustainability in Environmental Science, Sociology, Philosophy and Business Courses.

NASA Astrophysics Data System (ADS)

Boudrias, M. A.; Cantzler, J.; Croom, S.; Huston, C.; Woods, M.

2015-12-01

Courses on sustainability can be taught from multiple perspectives with some focused on specific areas (environmental, socio-cultural, economic, ethics) and others taking a more integrated approach across areas of sustainability and academic disciplines. In conjunction with the Climate Change Education Program efforts to enhance climate change literacy with innovative approaches, resources and communication strategies developed by Climate Education Partners were used in two distinct ways to integrate climate change science and impacts into undergraduate and graduate level courses. At the graduate level, the first lecture in the MBA program in Sustainable Supply Chain Management is entirely dedicated to climate change science, local and global impacts and discussions about key messages to communicate to the business community. Basic science concepts are integrated with discussions about mitigation and adaptation focused on business leaders. The concepts learned are then applied to the semester-long business plan project for the students. At the undergraduate level, a new model of comprehensive integration across disciplines was implemented in Spring 2015 across three courses on Sustainability each with a specific lens: Natural Science, Sociology and Philosophy. All three courses used climate change as the 'big picture' framing concept and had similar learning objectives creating a framework where lens-specific topics, focusing on depth in a discipline, were balanced with integrated exercises across disciplines providing breadth and possibilities for integration. The comprehensive integration project was the creation of the climate action plan for the university with each team focused on key areas of action (water, energy, transportation, etc.) and each team built with at least one member from each class ensuring a natural science, sociological and philosophical perspective. The final project was presented orally to all three classes and an integrated paper included all three perspectives. The best projects are being compiled so they can be shared with the University of San Diego's planning committee.

Using Maximum Entropy to Find Patterns in Genomes

NASA Astrophysics Data System (ADS)

Liu, Sophia; Hockenberry, Adam; Lancichinetti, Andrea; Jewett, Michael; Amaral, Luis

The existence of over- and under-represented sequence motifs in genomes provides evidence of selective evolutionary pressures on biological mechanisms such as transcription, translation, ligand-substrate binding, and host immunity. To accurately identify motifs and other genome-scale patterns of interest, it is essential to be able to generate accurate null models that are appropriate for the sequences under study. There are currently no tools available that allow users to create random coding sequences with specified amino acid composition and GC content. Using the principle of maximum entropy, we developed a method that generates unbiased random sequences with pre-specified amino acid and GC content. Our method is the simplest way to obtain maximally unbiased random sequences that are subject to GC usage and primary amino acid sequence constraints. This approach can also be easily be expanded to create unbiased random sequences that incorporate more complicated constraints such as individual nucleotide usage or even di-nucleotide frequencies. The ability to generate correctly specified null models will allow researchers to accurately identify sequence motifs which will lead to a better understanding of biological processes. National Institute of General Medical Science, Northwestern University Presidential Fellowship, National Science Foundation, David and Lucile Packard Foundation, Camille Dreyfus Teacher Scholar Award.

Writing Stories to Enhance Scientific Literacy

NASA Astrophysics Data System (ADS)

Ritchie, Stephen M.; Tomas, Louisa; Tones, Megan

2011-03-01

In response to international concerns about scientific literacy and students' waning interest in school science, this study investigated the effects of a science-writing project about the socioscientific issue (SSI) of biosecurity on the development of students' scientific literacy. Students generated two BioStories each that merged scientific information with the narrative storylines in the project. The study was conducted in two phases. In the exploratory phase, a qualitative case study of a sixth-grade class involving classroom observations and interviews informed the design of the second, confirmatory phase of the study, which was conducted at a different school. This phase involved a mixed methods approach featuring a quasi-experimental design with two classes of Australian middle school students (i.e., sixth grade, 11 years of age, n = 55). The results support the argument that writing the sequence of stories helped the students become more familiar with biosecurity issues, develop a deeper understanding of related biological concepts, and improve their interest in science. On the basis of these findings, teachers should be encouraged to engage their students in the practice of writing about SSI in a way that integrates scientific information into narrative storylines. Extending the practice to older students and exploring additional issues related to writing about SSI are recommended for further research.