Comparison and Validation of FLUKA and HZETRN as Tools for Investigating the Secondary Neutron Production in Large Space Vehicles

NASA Technical Reports Server (NTRS)

Rojdev, Kristina; Koontz, Steve; Reddell, Brandon; Atwell, William; Boeder, Paul

2015-01-01

NASA's exploration goals are focused on deep space travel and Mars surface operations. To accomplish these goals, large structures will be necessary to transport crew and logistics in the initial stages, and NASA will need to keep the crew and the vehicle safe during transport and any surface activities. One of the major challenges of deep space travel is the space radiation environment and its impacts on the crew, the electronics, and the vehicle materials. The primary radiation from the sun (solar particle events) and from outside the solar system (galactic cosmic rays) interact with materials of the vehicle. These interactions lead to some of the primary radiation being absorbed, being modified, or producing secondary radiation (primarily neutrons). With all vehicles, the high energy primary radiation is of most concern. However, with larger vehicles that have large shielding masses, there is more opportunity for secondary radiation production, and this secondary radiation can be significant enough to cause concern. When considering surface operations, there is also a secondary radiation source from the surface of the planet, known as albedo, with neutrons being one of the most significant species. Given new vehicle designs for deep space and Mars missions, the secondary radiation environment and the implications of that environment is currently not well understood. Thus, several studies are necessary to fill the knowledge gaps of this secondary radiation environment. In this paper, we put forth the initial steps to increasing our understanding of neutron production from large vehicles by comparing the neutron production resulting from our radiation transport codes and providing a preliminary validation of our results against flight data. This paper will review the details of these results and discuss the finer points of the analysis.

The Relationship between Classroom Organizational Structure and CRCT Performance in the Elementary School Classroom

ERIC Educational Resources Information Center

McClendon, Thomas K.

2016-01-01

This study examined the relationship between the structural classroom environment (self-contained, team-taught, and departmentalized) and student performance on the 2014 Georgia Criterion-Referenced Competency Test (CRCT) in reading, Language Arts, mathematics, science, and social studies in grades three through five. A secondary purpose examined…

RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis.

PubMed

Afzal, Muhammad; Shahid, Ahmad Ali; Shehzadi, Abida; Nadeem, Shahid; Husnain, Tayyab

2012-01-01

RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available. http://www.cemb.edu.pk/sw.html RDNAnalyzer - Random DNA Analyser, GUI - Graphical user interface, XAML - Extensible Application Markup Language.

Methods for isolation of marine-derived endophytic fungi and their bioactive secondary products.

PubMed

Kjer, Julia; Debbab, Abdessamad; Aly, Amal H; Proksch, Peter

2010-03-01

Marine-derived fungi have been shown in recent years to produce a plethora of new bioactive secondary metabolites, some of them featuring new carbon frameworks hitherto unprecedented in nature. These compounds are of interest as new lead structures for medicine as well as for plant protection. The aim of this protocol is to give a detailed description of methods useful for the isolation and cultivation of fungi associated with various marine organisms (sponges, algae and mangrove plants) for the extraction, characterization and structure elucidation of biologically active secondary metabolites produced by these marine-derived endophytic fungi, and for the preliminary evaluation of their pharmacological properties based on rapid 'in house' screening systems. Some results exemplifying the positive outcomes of the protocol are given at the end. From sampling in marine environment to completion of the structure elucidation and bioactivity screening, a period of at least 3 months has to be scheduled.

Solar Wind Access to Lunar Polar Craters: Feedback Between Surface Charging and Plasma Expansion

NASA Technical Reports Server (NTRS)

Zimmerman, M. I.; Farrell, W. M.; Stubbs, T. J.; Halekas, J. S.; Jackson, T. L.

2011-01-01

Determining the plasma environment within permanently shadowed lunar craters is critical to understanding local processes such as surface charging, electrostatic dust transport, volatile sequestration, and space weathering. In order to investigate the nature of this plasma environment, the first two-dimensional kinetic simulations of solar wind expansion into a lunar crater with a self-consistent plasma-surface interaction have been undertaken. The present results reveal how the plasma expansion into a crater couples with the electrically-charged lunar surface to produce a quasi-steady wake structure. In particular, there is a negative feedback between surface charging and ambipolar wake potential that allows an equilibrium to be achieved, with secondary electron emission strongly moderating the process. A range of secondary electron yields is explored, and two distinct limits are highlighted in which either surface charging or ambipoiar expansion is responsible for determining the overall wake structure.

Representing environment-induced helix-coil transitions in a coarse grained peptide model

NASA Astrophysics Data System (ADS)

Dalgicdir, Cahit; Globisch, Christoph; Sayar, Mehmet; Peter, Christine

2016-10-01

Coarse grained (CG) models are widely used in studying peptide self-assembly and nanostructure formation. One of the recurrent challenges in CG modeling is the problem of limited transferability, for example to different thermodynamic state points and system compositions. Understanding transferability is generally a prerequisite to knowing for which problems a model can be reliably used and predictive. For peptides, one crucial transferability question is whether a model reproduces the molecule's conformational response to a change in its molecular environment. This is of particular importance since CG peptide models often have to resort to auxiliary interactions that aid secondary structure formation. Such interactions take care of properties of the real system that are per se lost in the coarse graining process such as dihedral-angle correlations along the backbone or backbone hydrogen bonding. These auxiliary interactions may then easily overstabilize certain conformational propensities and therefore destroy the ability of the model to respond to stimuli and environment changes, i.e. they impede transferability. In the present paper we have investigated a short peptide with amphiphilic EALA repeats which undergoes conformational transitions between a disordered and a helical state upon a change in pH value or due to the presence of a soft apolar/polar interface. We designed a base CG peptide model that does not carry a specific (backbone) bias towards a secondary structure. This base model was combined with two typical approaches of ensuring secondary structure formation, namely a C α -C α -C α -C α pseudodihedral angle potential or a virtual site interaction that mimics hydrogen bonding. We have investigated the ability of the two resulting CG models to represent the environment-induced conformational changes in the helix-coil equilibrium of EALA. We show that with both approaches a CG peptide model can be obtained that is environment-transferable and that correctly represents the peptide's conformational response to different stimuli compared to atomistic reference simulations. The two types of auxiliary interactions lead to different kinetic behavior as well as to different structural properties for fully formed helices and folding intermediates, and we discuss the advantages and disadvantages of these approaches.

The Greening of Pesticide–Environment Interactions: Some Personal Observations

PubMed Central

2012-01-01

Background: Pesticide–environment interactions are bidirectional. The environment alters pesticides by metabolism and photodegradation, and pesticides in turn change the environment through nontarget or secondary effects. Objectives: Approximately 900 currently used commercial pesticides of widely diverse structures act by nearly a hundred mechanisms to control insects, weeds, and fungi, usually with minimal disruption of nature’s equilibrium. Here I consider some aspects of the discovery, development, and use of ecofriendly or green pesticides (i.e., pesticides that are safe, effective, and biodegradable with minimal adverse secondary effects on the environment). Emphasis is given to research in my laboratory. Discussion: The need for understanding and improving pesticide–environment interactions began with production of the first major insecticide approximately 150 years ago: The arsenical poison Paris Green was green in color but definitely not ecofriendly. Development and use of other pesticides has led to a variety of problems. Topics considered here include the need for high purity [e.g., hexachlorocyclohexane and polychloroborane isomers and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T)], environmental degradation and the bioactivity of resulting photoproducts and metabolites, pesticide photochemistry (including the use of structural optimization, photostabilizers, and photosensitizers to achieve suitable persistence), the presence of multiple active ingredients in botanical insecticides, the need to consider compounds with common mechanisms of action, issues related to primary and secondary targets, and chemically induced or genetically modified changes in plant biochemistry. Many insecticides are bird, fish, and honeybee toxicants, whereas herbicides and fungicides pose fewer environmental problems. Conclusion: Six factors have contributed to the greening of pesticide–environment interactions: advances in pesticide chemistry and toxicology, banning of many chlorinated hydrocarbons, the development of new biochemical targets, increased reliance on genetically modified crops that reduce the amount and variety of pesticides applied, emphasis on biodegradability and environmental protection, and integrated pest- and pesticide-management systems. PMID:22472325

Flight service environmental effects on composite materials and structures

NASA Technical Reports Server (NTRS)

Dexter, H. Benson; Baker, Donald J.

1992-01-01

NASA Langley and the U.S. Army have jointly sponsored programs to assess the effects of realistic flight environments and ground-based exposure on advanced composite materials and structures. Composite secondary structural components were initially installed on commercial transport aircraft in 1973; secondary and primary structural components were installed on commercial helicopters in 1979; and primary structural components were installed on commercial aircraft in the mid-to-late 1980's. Service performance, maintenance characteristics, and residual strength of numerous components are reported. In addition to data on flight components, 10 year ground exposure test results on material coupons are reported. Comparison between ground and flight environmental effects for several composite material systems are also presented. Test results indicate excellent in-service performance with the composite components during the 15 year period. Good correlation between ground-based material performance and operational structural performance has been achieved.

Fusion activity of HIV gp41 fusion domain is related to its secondary structure and depth of membrane insertion in a cholesterol-dependent fashion.

PubMed

Lai, Alex L; Moorthy, Anna Eswara; Li, Yinling; Tamm, Lukas K

2012-04-20

The human immunodeficiency virus (HIV) gp41 fusion domain plays a critical role in membrane fusion during viral entry. A thorough understanding of the relationship between the structure and the activity of the fusion domain in different lipid environments helps to formulate mechanistic models on how it might function in mediating membrane fusion. The secondary structure of the fusion domain in small liposomes composed of different lipid mixtures was investigated by circular dichroism spectroscopy.  The fusion domain formed an α-helix in membranes containing less than 30 mol% cholesterol and  formed β-sheet secondary structure in membranes containing ≥30 mol% cholesterol. EPR spectra of spin-labeled fusion domains also indicated different conformations in membranes with and without cholesterol. Power saturation EPR data were further used to determine the orientation and depth of α-helical fusion domains in lipid bilayers. Fusion and membrane perturbation activities of the gp41 fusion domain were measured by lipid mixing and contents leakage. The fusion domain fused membranes in both its helical form and its β-sheet form. High cholesterol, which induced β-sheets, promoted fusion; however, acidic lipids, which promoted relatively deep membrane insertion as an α-helix, also induced fusion. The results indicate that the structure of the HIV gp41 fusion domain is plastic and depends critically on the lipid environment. Provided that their membrane insertion is deep, α-helical and β-sheet conformations contribute to membrane fusion. Copyright © 2012 Elsevier Ltd. All rights reserved.

Sequence and conformational preferences at termini of α-helices in membrane proteins: role of the helix environment.

PubMed

Shelar, Ashish; Bansal, Manju

2014-12-01

α-Helices are amongst the most common secondary structural elements seen in membrane proteins and are packed in the form of helix bundles. These α-helices encounter varying external environments (hydrophobic, hydrophilic) that may influence the sequence preferences at their N and C-termini. The role of the external environment in stabilization of the helix termini in membrane proteins is still unknown. Here we analyze α-helices in a high-resolution dataset of integral α-helical membrane proteins and establish that their sequence and conformational preferences differ from those in globular proteins. We specifically examine these preferences at the N and C-termini in helices initiating/terminating inside the membrane core as well as in linkers connecting these transmembrane helices. We find that the sequence preferences and structural motifs at capping (Ncap and Ccap) and near-helical (N' and C') positions are influenced by a combination of features including the membrane environment and the innate helix initiation and termination property of residues forming structural motifs. We also find that a large number of helix termini which do not form any particular capping motif are stabilized by formation of hydrogen bonds and hydrophobic interactions contributed from the neighboring helices in the membrane protein. We further validate the sequence preferences obtained from our analysis with data from an ultradeep sequencing study that identifies evolutionarily conserved amino acids in the rat neurotensin receptor. The results from our analysis provide insights for the secondary structure prediction, modeling and design of membrane proteins. © 2014 Wiley Periodicals, Inc.

Launching Confident Numerate Learners

ERIC Educational Resources Information Center

Wade, Peter; Gervasoni, Ann; McQuade, Catharine; Smith, Catherine

2013-01-01

This paper explores how a secondary school in western Sydney used educational research as an impetus to change its mathematical education culture over a three year period. Key changes occurred in four areas: leadership; pedagogy; structures for teaching and learning; and mathematical environments. These included increased professional…

Transition to Post-Secondary Environments.

ERIC Educational Resources Information Center

Singh, Delar K.

This report discusses the findings of a national survey of 160 colleges and universities that explored facilities and services to students with orthopedic disabilities, including structural accessibility, academic accessibility, dorm-living, and recreational opportunities. Results of the survey indicate: (1) 10 percent of the institutions of…

RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis

PubMed Central

Afzal, Muhammad; Shahid, Ahmad Ali; Shehzadi, Abida; Nadeem, Shahid; Husnain, Tayyab

2012-01-01

RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available. Availability http://www.cemb.edu.pk/sw.html Abbreviations RDNAnalyzer - Random DNA Analyser, GUI - Graphical user interface, XAML - Extensible Application Markup Language. PMID:23055611

An Effect of the Learning Environment Management System toward Student Quality of Thai Secondary School

ERIC Educational Resources Information Center

Wirussawa, Seatuch; Tesaputa, Kowat; Duangpaeng, Amporn

2016-01-01

This study aimed at 1) investigating the element of the learning environment management system in the secondary schools, 2) exploring the current states and problems of the system on the learning environment management in the secondary schools, 3) designing the learning environment management system for the secondary schools, and 4) identifying…

Raman spectroscopic study of leptospiral glycolipoprotein

NASA Astrophysics Data System (ADS)

Bao, PeiDi; Bao, Lang; Huang, TianQuan; Liu, XinMing

1998-04-01

The Raman scattering spectra of two different samples of Leptospiral Glycoipoprotein (GLP-1 and GLP-2) which have different toxic effects have been obtained and investigated. Leptospirosis is one of the most harmful zoonosis. It is a serious public health issue in some area of Sichusan province. The two samples offer different structural informations of GLP molecules, it would be important to find the difference in contents, structures and the amino acid side - chains environment of the molecules between the two samples of GLP for understanding the different toxic effects. The intense Am I at 1651 cm-1 and weak Am III at 1283 cm-1 show that GLP-1 has a predominantly (alpha) -helix secondary structure. The intense Am I at 1674 cm-1 and intense Am III at 1246 cm-1 show that the conformation of GLP-2 has a high content of (Beta) - sheet and a low content of random - coil secondary structure. Strong Raman scattering occurs in the range 920- 980 cm-1, belong to the C-COO vibration and the stretching of the peptide backbone. The molecules of GLP-1 has trans-gauche-trans configuration of the C-S-S-C-C linkage and the molecules of GLP-2 has trans-gauche-gauche configuration of the C-C-S-S-C-C linkage. The intensity ratio of the two tyrosine liens at 830 cm-1 and 850 cm-1 is 1.1 and 1.23, indicate their tyrosine reduces environment respectively. Other side-chain environment in the two samples were discussed.

The Living With a Star Space Environment Testbed Experiments

NASA Technical Reports Server (NTRS)

Xapsos, Michael A.

2014-01-01

The focus of the Living With a Star (LWS) Space Environment Testbed (SET) program is to improve the performance of hardware in the space radiation environment. The program has developed a payload for the Air Force Research Laboratory (AFRL) Demonstration and Science Experiments (DSX) spacecraft that is scheduled for launch in August 2015 on the SpaceX Falcon Heavy rocket. The primary structure of DSX is an Evolved Expendable Launch Vehicle (EELV) Secondary Payload Adapter (ESPA) ring. DSX will be in a Medium Earth Orbit (MEO). This oral presentation will describe the SET payload.

The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling.

PubMed

Su, Ting; Cheng, Jingdong; Sohmen, Daniel; Hedman, Rickard; Berninghausen, Otto; von Heijne, Gunnar; Wilson, Daniel N; Beckmann, Roland

2017-05-30

Interaction between the nascent polypeptide chain and the ribosomal exit tunnel can modulate the rate of translation and induce translational arrest to regulate expression of downstream genes. The ribosomal tunnel also provides a protected environment for initial protein folding events. Here, we present a 2.9 Å cryo-electron microscopy structure of a ribosome stalled during translation of the extremely compacted VemP nascent chain. The nascent chain forms two α-helices connected by an α-turn and a loop, enabling a total of 37 amino acids to be observed within the first 50-55 Å of the exit tunnel. The structure reveals how α-helix formation directly within the peptidyltransferase center of the ribosome interferes with aminoacyl-tRNA accommodation, suggesting that during canonical translation, a major role of the exit tunnel is to prevent excessive secondary structure formation that can interfere with the peptidyltransferase activity of the ribosome.

Climate change and adaptational impacts in coastal systems: the case of sea defences.

PubMed

Firth, Louise B; Mieszkowska, Nova; Thompson, Richard C; Hawkins, Stephen J

2013-09-01

We briefly review how coastal ecosystems are responding to and being impacted by climate change, one of the greatest challenges facing society today. In adapting to rising and stormier seas associated with climate change, coastal defence structures are proliferating and becoming dominant coastal features, particularly in urbanised areas. Whilst the primary function of these structures is to protect coastal property and infrastructure, they inevitably have a significant secondary impact on the local environment and ecosystems. In this review we outline some of the negative and positive effects of these structures on physical processes, impacts on marine species, and the novel engineering approaches that have been employed to improve the ecological value of these structures in recent years. Finally we outline guidelines for an environmentally sensitive approach to design of such structures in the marine environment.

A Comparison and Contrast in Alternative Learning versus Traditional Learning

ERIC Educational Resources Information Center

Simmons, Mia A.

2013-01-01

Preparation for today's influenced technology professional world starts with structure of primary and secondary educational learning environments. The student learning platforms should be aligned in some ways to professional working platforms. This quantitative correlational ex post facto study compared the effectiveness of learning modalities in…

Prediction of Long Loops with Embedded Secondary Structure using the Protein Local Optimization Program

PubMed Central

Miller, Edward B.; Murrett, Colleen S.; Zhu, Kai; Zhao, Suwen; Goldfeld, Dahlia A.; Bylund, Joseph H.; Friesner, Richard A.

2013-01-01

Robust homology modeling to atomic-level accuracy requires in the general case successful prediction of protein loops containing small segments of secondary structure. Further, as loop prediction advances to success with larger loops, the exclusion of loops containing secondary structure becomes awkward. Here, we extend the applicability of the Protein Local Optimization Program (PLOP) to loops up to 17 residues in length that contain either helical or hairpin segments. In general, PLOP hierarchically samples conformational space and ranks candidate loops with a high-quality molecular mechanics force field. For loops identified to possess α-helical segments, we employ an alternative dihedral library composed of (ϕ,ψ) angles commonly found in helices. The alternative library is searched over a user-specified range of residues that define the helical bounds. The source of these helical bounds can be from popular secondary structure prediction software or from analysis of past loop predictions where a propensity to form a helix is observed. Due to the maturity of our energy model, the lowest energy loop across all experiments can be selected with an accuracy of sub-Ångström RMSD in 80% of cases, 1.0 to 1.5 Å RMSD in 14% of cases, and poorer than 1.5 Å RMSD in 6% of cases. The effectiveness of our current methods in predicting hairpin-containing loops is explored with hairpins up to 13 residues in length and again reaching an accuracy of sub-Ångström RMSD in 83% of cases, 1.0 to 1.5 Å RMSD in 10% of cases, and poorer than 1.5 Å RMSD in 7% of cases. Finally, we explore the effect of an imprecise surrounding environment, in which side chains, but not the backbone, are initially in perturbed geometries. In these cases, loops perturbed to 3Å RMSD from the native environment were restored to their native conformation with sub-Ångström RMSD. PMID:23814507

Project LEO Studies of Science Learning Environments and Outcomes, 1968-1981.

ERIC Educational Resources Information Center

Matthews, Charles; And Others

Presented is a summary of the 1977-80 Project LEO studies, which focused on science teaching strategies and learning outcomes for disruptive elementary school children and on more refined application of the "student-structured learning in science" (SSLS) teacher behavioral pattern in secondary school science classrooms. Included within…

Revised Guidelines for Comprehensive Health Education, Grades 10-12.

ERIC Educational Resources Information Center

Nebraska State Dept. of Education, Lincoln. Div. of Instructional Services.

These health curriculum guidelines were designed for teachers of secondary students. Four major topic areas are covered: 1) anatomy, physiology, tissues, systems, heredity, physical activity, and nutriition; 2) family structures, functions, and responsibilities; 3) values, stress, and drug abuse; and 4) the environment, disease control, cancer,…

Singapore Students' Misconceptions of Climate Change

ERIC Educational Resources Information Center

Chang, Chew-Hung; Pascua, Liberty

2016-01-01

Climate change is an important theme in the investigation of human-environment interactions in geographic education. This study explored the nature of students' understanding of concepts and processes related to climate change. Through semi-structured interviews, data was collected from 27 Secondary 3 (Grade 9) students from Singapore. The data…

Establishing a Taxonometric Structure for the Study of Biotechnology in Secondary School Technology Education.

ERIC Educational Resources Information Center

Wells, John G.

1994-01-01

A Delphi panel of 19 experts identified 8 main knowledge areas of biotechnology: bioprocessing, foundations, genetic engineering, agriculture, biochemistry, medicine, environment, and bioethics. Round 2 elicited 84 subdivisions and round 3 adjusted the ratings. The resulting classification suggests a different context and focus for technology…

Determination of the Molecular Structures of Ferric Enterobactin and Ferric Enantioenterobactin Using Racemic Crystallography.

PubMed

Johnstone, Timothy C; Nolan, Elizabeth M

2017-10-25

Enterobactin is a secondary metabolite produced by Enterobacteriaceae for acquiring iron, an essential metal nutrient. The biosynthesis and utilization of enterobactin permits many Gram-negative bacteria to thrive in environments where low soluble iron concentrations would otherwise preclude survival. Despite extensive work carried out on this celebrated molecule since its discovery over 40 years ago, the ferric enterobactin complex has eluded crystallographic structural characterization. We report the successful growth of single crystals containing ferric enterobactin using racemic crystallization, a method that involves cocrystallization of a chiral molecule with its mirror image. The structures of ferric enterobactin and ferric enantioenterobactin obtained in this work provide a definitive assignment of the stereochemistry at the metal center and reveal secondary coordination sphere interactions. The structures were employed in computational investigations of the interactions of these complexes with two enterobactin-binding proteins, which illuminate the influence of metal-centered chirality on these interactions. This work highlights the utility of small-molecule racemic crystallography for obtaining elusive structures of coordination complexes.

On the secondary eyewall formation of Hurricane Edouard (2014)

PubMed Central

Abarca, Sergio F.; Montgomery, Michael T.; Braun, Scott A.; Dunion, Jason

2018-01-01

A first observationally-based estimation of departures from gradient wind balance during secondary eyewall formation is presented. The study is based on the Atlantic Hurricane Edouard (2014). This storm was observed during the National Aeronautics and Space Administration’s (NASA) Hurricane and Severe Storm Sentinel (HS3) experiment, a field campaign conducted in collaboration with the National Oceanic and Atmospheric Administration (NOAA). A total of 135 dropsondes are analyzed in two separate time periods: one named the secondary eyewall formation period and the other one referred to as the decaying-double eyewalled storm period. During the secondary eyewall formation period, a time when the storm was observed to have only one eyewall, the diagnosed agradient force has a secondary maxima that coincides with the radial location of the secondary eyewall observed in the second period of study. The maximum spin up tendency of the radial influx of absolute vertical vorticity is within the boundary layer in the region of the eyewall of the storm and the spin up tendency structure elongates radially outward into the secondary region of supergradient wind, where the secondary wind maxima is observed in the second period of study. An analysis of the boundary-layer averaged vertical structure of equivalent potential temperature reveals a conditionally unstable environment in the secondary eyewall formation region. These findings support the hypothesis that deep convective activity in this region contributed to spin up of the boundary layer tangential winds and the formation of a secondary eyewall that is observed during the decaying-double eyewalled storm period. PMID:29651170

On the Secondary Eyewall Formation of Hurricane Edouard (2014)

NASA Technical Reports Server (NTRS)

Abarca, Sergio F.; Montgomery, Michael T.; Braun, Scott A.; Dunion, Jason

2016-01-01

A first observationally-based estimation of departures from gradient wind balance during secondary eyewall formation is presented. The study is based on the Atlantic Hurricane Edouard (2014). This storm was observed during the National Aeronautics and Space Administrations (NASA) Hurricane and Severe Storm Sentinel (HS3) experiment, a field campaign conducted in collaboration with the National Oceanic and Atmospheric Administration (NOAA). A total of 135 dropsondes are analyzed in two separate time periods: one named the secondary eyewall formation period and the other one referred to as the decaying-double eyewalled storm period. During the secondary eyewall formation period, a time when the storm was observed to have only one eyewall, the diagnosed agradient force has a secondary maxima that coincides with the radial location of the secondary eyewall observed in the second period of study. The maximum spin up tendency of the radial influx of absolute vertical vorticity is within the boundary layer in the region of the eyewall of the storm and the spin up tendency structure elongates radially outward into the secondary region of supergradient wind, where the secondary wind maxima is observed in the second period of study. An analysis of the boundary layer averaged vertical structure of equivalent potential temperature reveals a conditionally unstable environment in the secondary eyewall formation region. These findings support the hypothesis that deep convective activity in this region contributed to spin up of the boundary layer tangential winds and the formation of a secondary eyewall that is observed during the decaying-double eyewalled storm period.

On the secondary eyewall formation of Hurricane Edouard (2014).

PubMed

Abarca, Sergio F; Montgomery, Michael T; Braun, Scott A; Dunion, Jason

2016-09-01

A first observationally-based estimation of departures from gradient wind balance during secondary eyewall formation is presented. The study is based on the Atlantic Hurricane Edouard (2014). This storm was observed during the National Aeronautics and Space Administration's (NASA) Hurricane and Severe Storm Sentinel (HS3) experiment, a field campaign conducted in collaboration with the National Oceanic and Atmospheric Administration (NOAA). A total of 135 dropsondes are analyzed in two separate time periods: one named the secondary eyewall formation period and the other one referred to as the decaying-double eyewalled storm period. During the secondary eyewall formation period, a time when the storm was observed to have only one eyewall, the diagnosed agradient force has a secondary maxima that coincides with the radial location of the secondary eyewall observed in the second period of study. The maximum spin up tendency of the radial influx of absolute vertical vorticity is within the boundary layer in the region of the eyewall of the storm and the spin up tendency structure elongates radially outward into the secondary region of supergradient wind, where the secondary wind maxima is observed in the second period of study. An analysis of the boundary-layer averaged vertical structure of equivalent potential temperature reveals a conditionally unstable environment in the secondary eyewall formation region. These findings support the hypothesis that deep convective activity in this region contributed to spin up of the boundary layer tangential winds and the formation of a secondary eyewall that is observed during the decaying-double eyewalled storm period.

Biologically Active Secondary Metabolites from the Fungi.

PubMed

Bills, Gerald F; Gloer, James B

2016-11-01

Many Fungi have a well-developed secondary metabolism. The diversity of fungal species and the diversification of biosynthetic gene clusters underscores a nearly limitless potential for metabolic variation and an untapped resource for drug discovery and synthetic biology. Much of the ecological success of the filamentous fungi in colonizing the planet is owed to their ability to deploy their secondary metabolites in concert with their penetrative and absorptive mode of life. Fungal secondary metabolites exhibit biological activities that have been developed into life-saving medicines and agrochemicals. Toxic metabolites, known as mycotoxins, contaminate human and livestock food and indoor environments. Secondary metabolites are determinants of fungal diseases of humans, animals, and plants. Secondary metabolites exhibit a staggering variation in chemical structures and biological activities, yet their biosynthetic pathways share a number of key characteristics. The genes encoding cooperative steps of a biosynthetic pathway tend to be located contiguously on the chromosome in coregulated gene clusters. Advances in genome sequencing, computational tools, and analytical chemistry are enabling the rapid connection of gene clusters with their metabolic products. At least three fungal drug precursors, penicillin K and V, mycophenolic acid, and pleuromutilin, have been produced by synthetic reconstruction and expression of respective gene clusters in heterologous hosts. This review summarizes general aspects of fungal secondary metabolism and recent developments in our understanding of how and why fungi make secondary metabolites, how these molecules are produced, and how their biosynthetic genes are distributed across the Fungi. The breadth of fungal secondary metabolite diversity is highlighted by recent information on the biosynthesis of important fungus-derived metabolites that have contributed to human health and agriculture and that have negatively impacted crops, food distribution, and human environments.

Secondary Metabolites from Polar Organisms

PubMed Central

Tian, Yuan; Li, Yan-Ling; Zhao, Feng-Chun

2017-01-01

Polar organisms have been found to develop unique defences against the extreme environment environment, leading to the biosynthesis of novel molecules with diverse bioactivities. This review covers the 219 novel natural products described since 2001, from the Arctic and the Antarctic microoganisms, lichen, moss and marine faunas. The structures of the new compounds and details of the source organism, along with any relevant biological activities are presented. Where reported, synthetic and biosynthetic studies on the polar metabolites have also been included. PMID:28241505

Ecological Principles Affecting Community Structure and Secondary Production by Zooplankton in Marine and Freshwater Environments

DTIC Science & Technology

1988-01-01

Bialv~al can be common lipid -accumulating copepods or euphau- siids. The latitudinal trend in species rich- ness of freshwaters is the opposite...Cretaceous large- dinosaur com- er. For this reason it is most secure to focus munity (Oldman Formation). Ecology 57: 841- measurement effort on the

Classroom Environments and Student Empowerment: An Analysis of Elementary and Secondary Teacher Beliefs

ERIC Educational Resources Information Center

Nichols, Joe D.; Zhang, Guanglan

2011-01-01

This project explored a classroom model of motivation in which the source of student motivation is based on internal mechanisms or structures and classroom student/instructor interactions. It also extended earlier research in which beliefs of veteran, entry level, and preservice teachers have been explored. For this project, 117 elementary…

An Overview of the Characterization of the Space Launch Vehicle Aerodynamic Environments

NASA Technical Reports Server (NTRS)

Blevins, John A.; Campbell, John R., Jr.; Bennett, David W.; Rausch, Russ D.; Gomez, Reynaldo J.; Kiris, Cetin C.

2014-01-01

Aerodynamic environments are some of the rst engineering data products that are needed to design a space launch vehicle. These products are used in performance predic- tions, vehicle control algorithm design, as well as determing loads on primary and secondary structures in multiple discipline areas. When the National Aeronautics and Space Admin- istration (NASA) Space Launch System (SLS) Program was established with the goal of designing a new, heavy-lift launch vehicle rst capable of lifting the Orion Program Multi- Purpose Crew Vehicle (MPCV) to low-earth orbit and preserving the potential to evolve the design to a 200 metric ton cargo launcher, the data needs were no di erent. Upon commencement of the new program, a characterization of aerodynamic environments were immediately initiated. In the time since, the SLS Aerodynamics Team has produced data describing the majority of the aerodynamic environment de nitions needed for structural design and vehicle control under nominal ight conditions. This paper provides an overview of select SLS aerodynamic environments completed to date.

Sedimentary organic molecules: Origins and information content

NASA Technical Reports Server (NTRS)

Hayes, J. M.; Freeman, K. H.

1991-01-01

To progress in the study of organic geochemistry, we must dissect the processes controlling the composition of sedimentary organic matter. Structurally, this has proven difficult. Individual biomarkers can often be recognized, but their contribution to total organic materials is small, and their presence does not imply that their biochemical cell mates have survived. We are finding, however, that a combination of structural and isotopic lines of evidence provides new information. A starting point is provided by the isotopic compositions of primary products (degradation products of chlorophylls, alkenones derived from coccoliths). We find strong evidence that the isotopic difference between primary carbonate and algal organic material can be interpreted in terms of the concentration of dissolved CO2. Moreover, the isotopic difference between primary and total organic carbon can be interpreted in terms of characteristic isotopic shifts imposed by secondary processes (responsive, for example, to O2 levels in the depositional environment. In favorable cases, isotopic compositions of a variety of secondary products can be interpreted in terms of flows of carbon, and, therefore, in terms of specific processes and environmental conditions within the depositional environment.

An object programming based environment for protein secondary structure prediction.

PubMed

Giacomini, M; Ruggiero, C; Sacile, R

1996-01-01

The most frequently used methods for protein secondary structure prediction are empirical statistical methods and rule based methods. A consensus system based on object-oriented programming is presented, which integrates the two approaches with the aim of improving the prediction quality. This system uses an object-oriented knowledge representation based on the concepts of conformation, residue and protein, where the conformation class is the basis, the residue class derives from it and the protein class derives from the residue class. The system has been tested with satisfactory results on several proteins of the Brookhaven Protein Data Bank. Its results have been compared with the results of the most widely used prediction methods, and they show a higher prediction capability and greater stability. Moreover, the system itself provides an index of the reliability of its current prediction. This system can also be regarded as a basis structure for programs of this kind.

Magnesium-adenosine diphosphate binding sites in wild-type creatine kinase and in mutants: role of aromatic residues probed by Raman and infrared spectroscopies.

PubMed

Hagemann, H; Marcillat, O; Buchet, R; Vial, C

2000-08-08

Two distinct methods were used to investigate the role of Trp residues during Mg-ADP binding to cytosolic creatine kinase (CK) from rabbit muscle: (1) Raman spectroscopy, which is very sensitive to the environment of aromatic side-chain residues, and (2) reaction-induced infrared difference spectroscopy (RIDS) and photolabile substrate (ADP[Et(PhNO(2))]), combined with site-directed mutagenesis on the four Trp residues of CK. Our Raman results indicated that the environment of Trp and of Tyr were not affected during Mg-ADP binding to CK. Analysis of RIDS of wild-type CK, inactive W227Y, and active W210,217,272Y mutants suggested that Trp227 was not involved in the stacking interactions. Results are consistent with Trp227 being essential to prevent water molecules from entering in the active site [as suggested by Gross, M., Furter-Graves, E. M., Wallimann, T., Eppenberger, H. M., and Furter, R. (1994) Protein Sci. 3, 1058-1068] and that another Trp could in addition help to steer the nucleotide in the binding site, although it is not essential for the activity of CK. Raman and infrared spectra indicated that Mg-ADP binding does not involve large secondary structure changes. Only 3-4 residues absorbing in the amide I region are directly implicated in the Mg-ADP binding (corresponding to secondary structure changes less than 1%), suggesting that movement of protein domains due to Mg-nucleotide binding do not promote large secondary structure changes.

Effect of Anions on Nanofiber Formation of β-sheet Propensity Amphiphile Peptide

NASA Astrophysics Data System (ADS)

Shamsudeen, H.; Tan, H. L.; Eshak, Z.

2018-05-01

Peptide self-assembly forms different nanostructures under simple alteration in the solution environment. Understanding the mechanism of the assembly will help us to control and tailor functional nanomaterials. This study aims to investigate the influence of anions on the self-assembly morphology and shape using a synthetic peptide of FFFFKK. Circular Dichoism (CD) and Environmental Scanning Electron Microscope (ESEM) were used to determine the secondary structure and self-assembly morphology, while Image J imaging software was used to measure diameter size. In the absence of anion, FFFFKK formed anti-parallel β-sheet that adopted sizeable fibrillar structure with a minimal increment over the first 7 hours of assembly. Irregular structure was observed in the presence of Iodide ion (I-) with a less stable secondary structure such as β-turn and β-loop. In the presence of perchlorate ion (ClO4 -), needle-like structure was observed with predominantly β-sheet structure. Our study showed that peptide morphology can be controlled by using different anions with careful selection of amino acid residues in peptide sequence.

Evaluation of passive and active vibration control mechanisms in a microgravity environment

NASA Technical Reports Server (NTRS)

Ellison, J.; Ahmadi, G.; Grodsinsky, C.

1993-01-01

The behavior of equipment and their light secondary attachments in large space structures under orbital excitation is studied. The equipment is modeled as a shear beam and its secondary attachment is treated as a single-degree-of-freedom lumped mass system. Peak responses of the equipment and its secondary system for a variety of vibration control mechanisms are evaluated. A novel active friction control mechanism, by varying the normal force, is suggested. The device uses a magnetic field control to minimize the stick condition, thereby reducing the overall structural response. The results show that the use of the passive vibration control devices could reduce the peak equipment responses to a certain extent. However, major reduction of vibration levels could be achieved only by the use of active devices. Using active control of the interface normal force, the peak responses of the equipment and its attachment are reduced by a factor of 10 over the fixed-base equipment response.

Examining the emerging entrepreneurial mindset in adolescence: A study in Nigeria.

PubMed

Salami, Samuel O

2017-05-10

This study investigated the relationship of family environment, network, parental socio-economic status, self-efficacy and proactive personality on entrepreneurial intention of secondary school adolescents and the mediating role of self-efficacy. The participants were 250 secondary school SS2 adolescents randomly selected from six secondary schools in Ibadan Metropolis, Ibadan, Oyo State, Nigeria. Structural Equation Modelling was used to analyse the data obtained from the participants. The results showed that all the contextual and individual factors had significant relationship with entrepreneurial intention and self-efficacy partially mediated the relationship. It was suggested that counselling psychologists should consider the contextual and individual variables while assisting students in building their entrepreneurial intention. © 2017 International Union of Psychological Science.

Pharmaceutically active secondary metabolites of marine actinobacteria.

PubMed

Manivasagan, Panchanathan; Venkatesan, Jayachandran; Sivakumar, Kannan; Kim, Se-Kwon

2014-04-01

Marine actinobacteria are one of the most efficient groups of secondary metabolite producers and are very important from an industrial point of view. Many representatives of the order Actinomycetales are prolific producers of thousands of biologically active secondary metabolites. Actinobacteria from terrestrial sources have been studied and screened since the 1950s, for many important antibiotics, anticancer, antitumor and immunosuppressive agents. However, frequent rediscovery of the same compounds from the terrestrial actinobacteria has made them less attractive for screening programs in the recent years. At the same time, actinobacteria isolated from the marine environment have currently received considerable attention due to the structural diversity and unique biological activities of their secondary metabolites. They are efficient producers of new secondary metabolites that show a range of biological activities including antibacterial, antifungal, anticancer, antitumor, cytotoxic, cytostatic, anti-inflammatory, anti-parasitic, anti-malaria, antiviral, antioxidant, anti-angiogenesis, etc. In this review, an evaluation is made on the current status of research on marine actinobacteria yielding pharmaceutically active secondary metabolites. Bioactive compounds from marine actinobacteria possess distinct chemical structures that may form the basis for synthesis of new drugs that could be used to combat resistant pathogens. With the increasing advancement in science and technology, there would be a greater demand for new bioactive compounds synthesized by actinobacteria from various marine sources in future. Copyright © 2013 Elsevier GmbH. All rights reserved.

The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling

PubMed Central

Su, Ting; Cheng, Jingdong; Sohmen, Daniel; Hedman, Rickard; Berninghausen, Otto; von Heijne, Gunnar; Wilson, Daniel N; Beckmann, Roland

2017-01-01

Interaction between the nascent polypeptide chain and the ribosomal exit tunnel can modulate the rate of translation and induce translational arrest to regulate expression of downstream genes. The ribosomal tunnel also provides a protected environment for initial protein folding events. Here, we present a 2.9 Å cryo-electron microscopy structure of a ribosome stalled during translation of the extremely compacted VemP nascent chain. The nascent chain forms two α-helices connected by an α-turn and a loop, enabling a total of 37 amino acids to be observed within the first 50–55 Å of the exit tunnel. The structure reveals how α-helix formation directly within the peptidyltransferase center of the ribosome interferes with aminoacyl-tRNA accommodation, suggesting that during canonical translation, a major role of the exit tunnel is to prevent excessive secondary structure formation that can interfere with the peptidyltransferase activity of the ribosome. DOI: http://dx.doi.org/10.7554/eLife.25642.001 PMID:28556777

40 CFR 133.105 - Treatment equivalent to secondary treatment.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 23 2012-07-01 2012-07-01 false Treatment equivalent to secondary treatment. 133.105 Section 133.105 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS SECONDARY TREATMENT REGULATION § 133.105 Treatment equivalent to secondary treatment...

40 CFR 133.102 - Secondary treatment.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 23 2012-07-01 2012-07-01 false Secondary treatment. 133.102 Section 133.102 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS SECONDARY TREATMENT REGULATION § 133.102 Secondary treatment. The following paragraphs describe the minimum level of...

On the Use of 3dB Qualification Margin for Structural Parts on Expendable Launch Vehicles

NASA Technical Reports Server (NTRS)

Yunis, Isam

2007-01-01

The standard random vibration qualification test used for Expendable Launch Vehicle components is Maximum Predicted Environment (MPE) + 6dB for a duration of 4 times the service life of the part. This can be a severe qualification test for these fatigue-sensitive structures. This paper uses flight data from several launch vehicles to establish that reducing the qualification approach to MPE+3dB for the duration of the peak environment (1x life) is valid for fatigue-sensitive structural components. Items that can be classified as fatigue-sensitive are probes, ducts, tubing, bellows, hoses, and any non-functional structure. Non-functional structure may be flight critical or carry fluid, but it cannot include any moving parts or electronics. This reduced qualification approach does not include primary or secondary structure which would be exclusively designed by peak loads, either transient or quasi-static, that are so large and of so few cycles as to make fatigue a moot point.

Multiple-probe analysis of folding and unfolding pathways of human serum albumin. Evidence for a framework mechanism of folding.

PubMed

Santra, Manas Kumar; Banerjee, Abhijit; Krishnakumar, Shyam Sundar; Rahaman, Obaidur; Panda, Dulal

2004-05-01

The changes in the far-UV CD signal, intrinsic tryptophan fluorescence and bilirubin absorbance showed that the guanidine hydrochloride (GdnHCl)-induced unfolding of a multidomain protein, human serum albumin (HSA), followed a two-state process. However, using environment sensitive Nile red fluorescence, the unfolding and folding pathways of HSA were found to follow a three-state process and an intermediate was detected in the range 0.25-1.5 m GdnHCl. The intermediate state displayed 45% higher fluorescence intensity than that of the native state. The increase in the Nile red fluorescence was found to be due to an increase in the quantum yield of the HSA-bound Nile red. Low concentrations of GdnHCl neither altered the binding affinity of Nile red to HSA nor induced the aggregation of HSA. In addition, the secondary structure of HSA was not perturbed during the first unfolding transition (<1.5 m GdnHCl); however, the secondary structure was completely lost during the second transition. The data together showed that the half maximal loss of the tertiary structure occurred at a lower GdnHCl concentration than the loss of the secondary structure. Further kinetic studies of the refolding process of HSA using multiple spectroscopic techniques showed that the folding occurred in two phases, a burst phase followed by a slow phase. An intermediate with native-like secondary structure but only a partial tertiary structure was found to form in the burst phase of refolding. Then, the intermediate slowly folded into the native state. An analysis of the refolding data suggested that the folding of HSA could be best explained by the framework model.

The Dinosaur in the Classroom: What We Stand to Lose through Ability-Grouping in the Primary School

ERIC Educational Resources Information Center

Marks, Rachel

2014-01-01

Embedding setting (subject-based ability-grouping) into the primary school environment creates structural conflict--physically and culturally--fundamentally changing the nature of primary schools through the imposition of secondary practices and cultures and the loss of pastoral care. This article examines the hidden implications for teachers and…

PB1-F2 Influenza A Virus Protein Adopts a β-Sheet Conformation and Forms Amyloid Fibers in Membrane Environments

PubMed Central

Chevalier, Christophe; Al Bazzal, Ali; Vidic, Jasmina; Février, Vincent; Bourdieu, Christiane; Bouguyon, Edwige; Le Goffic, Ronan; Vautherot, Jean-François; Bernard, Julie; Moudjou, Mohammed; Noinville, Sylvie; Chich, Jean-François; Da Costa, Bruno; Rezaei, Human; Delmas, Bernard

2010-01-01

The influenza A virus PB1-F2 protein, encoded by an alternative reading frame in the PB1 polymerase gene, displays a high sequence polymorphism and is reported to contribute to viral pathogenesis in a sequence-specific manner. To gain insights into the functions of PB1-F2, the molecular structure of several PB1-F2 variants produced in Escherichia coli was investigated in different environments. Circular dichroism spectroscopy shows that all variants have a random coil secondary structure in aqueous solution. When incubated in trifluoroethanol polar solvent, all PB1-F2 variants adopt an α-helix-rich structure, whereas incubated in acetonitrile, a solvent of medium polarity mimicking the membrane environment, they display β-sheet secondary structures. Incubated with asolectin liposomes and SDS micelles, PB1-F2 variants also acquire a β-sheet structure. Dynamic light scattering revealed that the presence of β-sheets is correlated with an oligomerization/aggregation of PB1-F2. Electron microscopy showed that PB1-F2 forms amorphous aggregates in acetonitrile. In contrast, at low concentrations of SDS, PB1-F2 variants exhibited various abilities to form fibers that were evidenced as amyloid fibers in a thioflavin T assay. Using a recombinant virus and its PB1-F2 knock-out mutant, we show that PB1-F2 also forms amyloid structures in infected cells. Functional membrane permeabilization assays revealed that the PB1-F2 variants can perforate membranes at nanomolar concentrations but with activities found to be sequence-dependent and not obviously correlated with their differential ability to form amyloid fibers. All of these observations suggest that PB1-F2 could be involved in physiological processes through different pathways, permeabilization of cellular membranes, and amyloid fiber formation. PMID:20172856

PB1-F2 influenza A virus protein adopts a beta-sheet conformation and forms amyloid fibers in membrane environments.

PubMed

Chevalier, Christophe; Al Bazzal, Ali; Vidic, Jasmina; Février, Vincent; Bourdieu, Christiane; Bouguyon, Edwige; Le Goffic, Ronan; Vautherot, Jean-François; Bernard, Julie; Moudjou, Mohammed; Noinville, Sylvie; Chich, Jean-François; Da Costa, Bruno; Rezaei, Human; Delmas, Bernard

2010-04-23

The influenza A virus PB1-F2 protein, encoded by an alternative reading frame in the PB1 polymerase gene, displays a high sequence polymorphism and is reported to contribute to viral pathogenesis in a sequence-specific manner. To gain insights into the functions of PB1-F2, the molecular structure of several PB1-F2 variants produced in Escherichia coli was investigated in different environments. Circular dichroism spectroscopy shows that all variants have a random coil secondary structure in aqueous solution. When incubated in trifluoroethanol polar solvent, all PB1-F2 variants adopt an alpha-helix-rich structure, whereas incubated in acetonitrile, a solvent of medium polarity mimicking the membrane environment, they display beta-sheet secondary structures. Incubated with asolectin liposomes and SDS micelles, PB1-F2 variants also acquire a beta-sheet structure. Dynamic light scattering revealed that the presence of beta-sheets is correlated with an oligomerization/aggregation of PB1-F2. Electron microscopy showed that PB1-F2 forms amorphous aggregates in acetonitrile. In contrast, at low concentrations of SDS, PB1-F2 variants exhibited various abilities to form fibers that were evidenced as amyloid fibers in a thioflavin T assay. Using a recombinant virus and its PB1-F2 knock-out mutant, we show that PB1-F2 also forms amyloid structures in infected cells. Functional membrane permeabilization assays revealed that the PB1-F2 variants can perforate membranes at nanomolar concentrations but with activities found to be sequence-dependent and not obviously correlated with their differential ability to form amyloid fibers. All of these observations suggest that PB1-F2 could be involved in physiological processes through different pathways, permeabilization of cellular membranes, and amyloid fiber formation.

Reliability and Validity towards Environment Attitude Scale for Secondary School Students

ERIC Educational Resources Information Center

Uzunoz, Abdulkadir

2011-01-01

This research, tries to develop an attitude scale (educational access schemes (EAS) for SS) which determines the approaches of secondary students for environment. First 400 secondary students were invited to write a composition named "The importance of environment and its position in our lives". The compositions were examined one by one…

alpha-helical structural elements within the voltage-sensing domains of a K(+) channel.

PubMed

Li-Smerin, Y; Hackos, D H; Swartz, K J

2000-01-01

Voltage-gated K(+) channels are tetramers with each subunit containing six (S1-S6) putative membrane spanning segments. The fifth through sixth transmembrane segments (S5-S6) from each of four subunits assemble to form a central pore domain. A growing body of evidence suggests that the first four segments (S1-S4) comprise a domain-like voltage-sensing structure. While the topology of this region is reasonably well defined, the secondary and tertiary structures of these transmembrane segments are not. To explore the secondary structure of the voltage-sensing domains, we used alanine-scanning mutagenesis through the region encompassing the first four transmembrane segments in the drk1 voltage-gated K(+) channel. We examined the mutation-induced perturbation in gating free energy for periodicity characteristic of alpha-helices. Our results are consistent with at least portions of S1, S2, S3, and S4 adopting alpha-helical secondary structure. In addition, both the S1-S2 and S3-S4 linkers exhibited substantial helical character. The distribution of gating perturbations for S1 and S2 suggest that these two helices interact primarily with two environments. In contrast, the distribution of perturbations for S3 and S4 were more complex, suggesting that the latter two helices make more extensive protein contacts, possibly interfacing directly with the shell of the pore domain.

Vertebrate reservoirs and secondary epidemiological cycles of vector-borne diseases.

PubMed

Kock, R A

2015-04-01

Vector-borne diseases of importance to human and domestic animal health are listed and the increasing emergence of syndromes, new epidemiological cycles and distributions are highlighted. These diseases involve a multitude of vectors and hosts, frequently for the same pathogen, and involve natural enzootic cycles, wild reservoirs and secondary epidemiological cycles, sometimes affecting humans and domestic animals. On occasions the main reservoir is in the domestic environment. Drivers for secondary cycles are mainly related to human impacts and activities and therefore, for purposes of prevention and control, the focus needs to be on the socioecology of the diseases. Technical and therapeutical solutions exist, and for control there needs to be a clear understanding of the main vertebrate hosts or reservoirs and the main vectors. The targets of interventions are usually the vector and/or secondary epidemiological cycles and, in the case of humans and domestic animals, the spillover or incidental hosts are treated. More attention needs to be given to the importance of the political economy in relation to vector-borne diseases, as many key drivers arise from globalisation, climate change and changes in structural ecologies. Attention to reducing the risk of emergence of new infection cycles through better management of the human-animal-environment interface is urgently needed.

Lamont-Doherty's Secondary School Field Research Program: Institutionalizing outreach to secondary school students at a soft-money research institute

NASA Astrophysics Data System (ADS)

Sambrotto, R.

2015-12-01

The Secondary School Field Research Program is a field and laboratory internship for high school students at the Lamont-Doherty Earth Observatory. Over the past 11 years it has grown into a significant program, engaging approximately 50 high school and college students each summer, most of them from ethnic and economic groups that are under-represented in the STEM fields. The internships are based on research-driven science questions on estuarine physics, chemistry, ecology and the paleo-environment. Field studies are linked to associated laboratory analyses whose results are reported by the students as a final project. For the past two years, we have focused on the transition to an institutional program, with sustainable funding and organizational structures. At a grant-driven institution whose mission is largely restricted to basic research, institutionalization has not been an easy task. To leverage scarce resources we have implemented a layered structure that relies on near-peer mentoring. So a typical research team might include a mix of new and more experienced high school students, a college student, a high school science teacher and a Lamont researcher as a mentor. Graduates of the program are employed to assist with administration. Knowledge and best practices diffuse through the organization in an organic, if not entirely structured, fashion. We have found that a key to long-term funding has been survival: as we have sustained a successful program and developed a model adapted to Lamont's unique environment, we have attracted longer term core financing on which grant-driven extensions can be built. The result is a highly flexible program that is student-centered in the context of a broader research culture connecting our participants with the advantages of working at a premier soft-money research institution.

Characterizing Secondary Debris Impact Ejecta

NASA Technical Reports Server (NTRS)

Schonberg, W. P.

1999-01-01

All spacecraft in low-Earth orbit are subject to high-speed impacts by meteoroids and orbital debris particles. These impacts can damage flight-critical systems which can in turn lead to catastrophic failure of the spacecraft. Therefore, the design of a spacecraft for an Earth-orbiting mission must take into account the possibility of such impacts and their effects on the spacecraft structure and on all of its exposed subsystem components. In addition to threatening the operation of the spacecraft itself, on-orbit impacts also generate a significant amount of ricochet particles. These high-speed particles can destroy critical external spacecraft subsystem and also increase the contamination of the orbital environment. This report presents a summary of the work performed towards the development of an empirical model that characterizes the secondary ejecta created by a high-speed impacta on a typical aerospace structural surface.

Paul Revere Rides through High School Government Class: Teacher Research and the Power of Discussion to Motivate Thinking

ERIC Educational Resources Information Center

Newstreet, Carmen

2008-01-01

Teachers in the secondary social studies classroom do not regularly take the time to practice structured reflection on their teaching methods. In our current standards-driven environment, social studies classrooms are often not seen as places of higher learning. To combat these stereotypes, the author presents a method for accomplishing reflection…

A semi-supervised learning approach for RNA secondary structure prediction.

PubMed

Yonemoto, Haruka; Asai, Kiyoshi; Hamada, Michiaki

2015-08-01

RNA secondary structure prediction is a key technology in RNA bioinformatics. Most algorithms for RNA secondary structure prediction use probabilistic models, in which the model parameters are trained with reliable RNA secondary structures. Because of the difficulty of determining RNA secondary structures by experimental procedures, such as NMR or X-ray crystal structural analyses, there are still many RNA sequences that could be useful for training whose secondary structures have not been experimentally determined. In this paper, we introduce a novel semi-supervised learning approach for training parameters in a probabilistic model of RNA secondary structures in which we employ not only RNA sequences with annotated secondary structures but also ones with unknown secondary structures. Our model is based on a hybrid of generative (stochastic context-free grammars) and discriminative models (conditional random fields) that has been successfully applied to natural language processing. Computational experiments indicate that the accuracy of secondary structure prediction is improved by incorporating RNA sequences with unknown secondary structures into training. To our knowledge, this is the first study of a semi-supervised learning approach for RNA secondary structure prediction. This technique will be useful when the number of reliable structures is limited. Copyright © 2015 Elsevier Ltd. All rights reserved.

[The structure of vegetative organs, and saponins histochemical localization and content comparization in Polygala sibirica L].

PubMed

Teng, Hong Mei; Fang, Min Feng; Hu, Zheng Hai

2009-02-01

Anatomical, histochemical and phytochemistry methods were used to investigate the structure of vegetative organs, and saponins localization and dynamic changes in Polygala sibirica L. The root consisted of developed periderm and secondary vascular. The secondary phloem was thick, and mainly composed of parenchyma. There were well-developed vessels and fibers in the secondary xylem. The stem was composed of epidermis, cortex and vascular bundle. The ring of sclerenchymatous cells lied between cortex and phloem might be the apoplastic protective screen which could protect the stem from drought. The leaf was bifacial one. The root and stem possessed characteristics adapting to arid environment. Histochemical localization results showed that saponins distributed in secondary phloem and phelloderm of root, in epidermis, cortex and phloem of stem, mainly in mesophyll of leaf. It displayed that saponins accumulated mainly in parenchyma cells of vegetative organs, among of which, the secondary phloem was the main storage site. The HPLC results also showed that the saponins accumulated in all the vegetative organs of Polygala sibirica L., with higher content in roots and lower content in the aerial part that included stems and leaves. The study indicated the aerial part of Polygala sibirica L. also had medicinal value. The saponins content had dynamic variance at the developmental stage, the crude drug should be gathered at period from April to May.

SERS+MEF of the anti-tumoral drug emodin adsorbed on silver nanoparticles

NASA Astrophysics Data System (ADS)

Sevilla, Paz; De Llanos, Raquel; Domingo, Concepción; Sánchez-Cortés, Santiago; García-Ramos, José V.

2010-02-01

Metal nanostructures are known to amplify the spontaneous emission of fluorescent molecules by resonant coupling to external electromagnetic fields. We have used spectroscopy to characterize the structural properties of emodin molecules, a natural anthraquinone dye, and bovine serum albumin, the most abundant protein in plasma, in the presence of silver nanoparticles. Aggregation of emodin at pH=10 and pH=6 gives rise to SERS and MEF effects in silver colloid. We have obtained MEF spectra at acidic pH=2.9 using two different silver nanostructures. We have also studied the change in the secondary structure of bovine serum albumin adsorbed on metal nanoparticles surface. Circular dichroism, fluorescence emission and fluorescence lifetime measurements indicate an increase in the alfa-helical content of the protein and a change in the environment of the tryptophan residues that bury in the interior of the biomolecule. This variation on the secondary structure could have further influence in the binding of the drug to form transport and regulatory complexes.

ATP-induced noncooperative thermal unfolding of hen lysozyme

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

Liu, Honglin; Yin, Peidong; He, Shengnan

To understand the role of ATP underlying the enhanced amyloidosis of hen egg white lysozyme (HEWL), the synchrotron radiation circular dichroism, combined with tryptophan fluorescence, dynamic light-scattering, and differential scanning calorimetry, is used to examine the alterations of the conformation and thermal unfolding pathway of the HEWL in the presence of ATP, Mg{sup 2+}-ATP, ADP, AMP, etc. It is revealed that the binding of ATP to HEWL through strong electrostatic interaction changes the secondary structures of HEWL and makes the exposed residue W62 move into hydrophobic environments. This alteration of W62 decreases the {beta}-domain stability of HEWL, induces a noncooperativemore » unfolding of the secondary structures, and produces a partially unfolded intermediate. This intermediate containing relatively rich {alpha}-helix and less {beta}-sheet structures has a great tendency to aggregate. The results imply that the ease of aggregating of HEWL is related to the extent of denaturation of the amyloidogenic region, rather than the electrostatic neutralizing effect or monomeric {beta}-sheet enriched intermediate.« less

Patient-centered knowledge sharing in healthcare organizations: Identifying the external barriers.

PubMed

Zhou, Lihong

2017-12-01

This paper reports on a research study, which aims to identify, qualify, and theorize the external barriers that prevent and hinder the exercises and activities of patient-centered knowledge sharing (KS) in healthcare organizations. The project adopted a qualitative secondary analysis approach as the overarching methodology to guide the analysis of data collected in a previously completed research study. Specifically, 46 semi-structured interview data were included and analyzed using a thematic analysis approach. The secondary analysis showed that healthcare KS is strongly influenced and hindered by five external barriers: social belief and preference, cultural values, healthcare education structure, political decisions, and economic environment and constraints. Moreover, the research findings suggest that these external barriers cannot be overlooked in KS implementation and operation in healthcare organizations and should be carefully assessed beginning in the early stages of KS design and strategic planning. Based on the secondary analysis, this paper proposes a conceptual model, which will contribute to the development of hypotheses in the future for building a generalized knowledge. The case study used is Chinese healthcare, but the KS problems studied can be shared across international borders.

Operating a petabyte class archive at ESO

NASA Astrophysics Data System (ADS)

Suchar, Dieter; Lockhart, John S.; Burrows, Andrew

2008-07-01

The challenges of setting up and operating a Petabyte Class Archive will be described in terms of computer systems within a complex Data Centre environment. The computer systems, including the ESO Primary and Secondary Archive and the associated computational environments such as relational databases will be explained. This encompasses the entire system project cycle, including the technical specifications, procurement process, equipment installation and all further operational phases. The ESO Data Centre construction and the complexity of managing the environment will be presented. Many factors had to be considered during the construction phase, such as power consumption, targeted cooling and the accumulated load on the building structure to enable the smooth running of a Petabyte class Archive.

Overview of SLS Aeroacoustic Environment Development

NASA Technical Reports Server (NTRS)

Steva, Thomas; Herron, Andrew

2017-01-01

The Space Launch System (SLS) ascent aeroacoustic environments provide the externally driven noise levels predicted for vehicle ascent during transonic and supersonic flight, and serve as an important input for component and secondary structure vibroacoustic design criteria. This aerodynamically induced noise is predominantly generated by unsteady flow within the local boundary layer due to free stream interaction with the outer mold line (OML). Additional sources are shear flow interactions, shocks, protuberance flows, and wake flows. This presentation provides an overview of the aeroacoustics discipline along with the SLS environment development process, including wind tunnel testing and general data reduction methods. The state of the discipline is also presented with a summary of aeroacoustic measurement and computational techniques currently on the horizon.

Drag reduction using metallic engineered surfaces with highly ordered hierarchical topographies: nanostructures on micro-riblets

NASA Astrophysics Data System (ADS)

Kim, Taekyung; Shin, Ryung; Jung, Myungki; Lee, Jinhyung; Park, Changsu; Kang, Shinill

2016-03-01

Durable drag-reduction surfaces have recently received much attention, due to energy-saving and power-consumption issues associated with harsh environment applications, such as those experienced by piping infrastructure, ships, aviation, underwater vehicles, and high-speed ground vehicles. In this study, a durable, metallic surface with highly ordered hierarchical structures was used to enhance drag-reduction properties, by combining two passive drag-reduction strategies: an air-layer effect induced by nanostructures and secondary vortex generation by micro-riblet structures. The nanostructures and micro-riblet structures were designed to increase slip length. The top-down fabrication method used to form the metallic hierarchical structures combined laser interference lithography, photolithography, thermal reflow, nanoimprinting, and pulse-reverse-current electrochemical deposition. The surfaces were formed from nickel, which has high hardness and corrosion resistance, making it suitable for use in harsh environments. The drag-reduction properties of various metal surfaces were investigated based on the surface structure: a bare surface, a nanostructured surface, a micro-riblet surface, and a hierarchically structured surface of nanostructures on micro-riblets.

RNA-SSPT: RNA Secondary Structure Prediction Tools.

PubMed

Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; Din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

2013-01-01

The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes.

RNA-SSPT: RNA Secondary Structure Prediction Tools

PubMed Central

Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

2013-01-01

The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes. PMID:24250115

An Instrument for Investigating Chinese Language Learning Environments in Singapore Secondary Schools

ERIC Educational Resources Information Center

Chua, Siew Lian; Wong, Angela F. L.; Chen, Der-Thanq

2009-01-01

This paper describes how a new classroom environment instrument, the "Chinese Language Classroom Environment Inventory (CLCEI)", was developed to investigate the nature of Chinese language classroom learning environments in Singapore secondary schools. The CLCEI is a bilingual instrument (English and Chinese Language) with 48 items…

Psychosocial Environment and Student Self-Handicapping in Secondary School Mathematics Classes: A Cross-National Study.

ERIC Educational Resources Information Center

Dorman, Jeffrey P.; Adams, Joan E.; Ferguson, Janet M.

2002-01-01

Presents an investigation of the relationship between classroom environment and self-handicapping in Australian, Canadian, and British secondary schools. Explores student perceptions of classroom environment, self-handicapping, and academic efficacy. Reports that classroom environment scales accounted for variance in self-handicapping beyond what…

α-Helical Structural Elements within the Voltage-Sensing Domains of a K+ Channel

PubMed Central

Li-Smerin, Yingying; Hackos, David H.; Swartz, Kenton J.

2000-01-01

Voltage-gated K+ channels are tetramers with each subunit containing six (S1–S6) putative membrane spanning segments. The fifth through sixth transmembrane segments (S5–S6) from each of four subunits assemble to form a central pore domain. A growing body of evidence suggests that the first four segments (S1–S4) comprise a domain-like voltage-sensing structure. While the topology of this region is reasonably well defined, the secondary and tertiary structures of these transmembrane segments are not. To explore the secondary structure of the voltage-sensing domains, we used alanine-scanning mutagenesis through the region encompassing the first four transmembrane segments in the drk1 voltage-gated K+ channel. We examined the mutation-induced perturbation in gating free energy for periodicity characteristic of α-helices. Our results are consistent with at least portions of S1, S2, S3, and S4 adopting α-helical secondary structure. In addition, both the S1–S2 and S3–S4 linkers exhibited substantial helical character. The distribution of gating perturbations for S1 and S2 suggest that these two helices interact primarily with two environments. In contrast, the distribution of perturbations for S3 and S4 were more complex, suggesting that the latter two helices make more extensive protein contacts, possibly interfacing directly with the shell of the pore domain. PMID:10613917

Secondary Traumatic Stress and Burnout of North Korean Refugees Service Providers.

PubMed

Kim, Yeunhee Joyce

2017-03-01

The current study investigated the burnout and secondary traumatic stress of service providers for North Korean (NK) refugees based on the conceptual framework of theJob Demands-Resources (JD-R) model of workplace burnout. A cross-sectional self-administered survey was conducted with a national sample consisting of all 63 organizations in direct services to North Korean refugees. Of the estimated total number of 230 service providers comprising of social workers, psychotherapists, job counselors and paraprofessional counselors, 179 completed the survey, a 77.8% return rate. While job resources such as personal commitment to work and organizational support indicated inverse relations to burnout, job demands such as workload, work environment and secondary traumatic stress (STS) showed a positive relationship to worker burnout. The STS were present in more than half of the respondents (51.3%), of which 20.7% of them indicating a severe level of STS. The STS proved to be the most significant risk to worker burnout as it showed strong relations to all three dimensions of burnout. Structural issues of chronic work overload and poor work environment need to be addressed to reduce staff burnout. STS is a serious occupational hazard in working with North Korean refugees.

Corrosion inhibition of steam generator tubesheet by Alloy 690 cladding in secondary side environments

NASA Astrophysics Data System (ADS)

Hur, Do Haeng; Choi, Myung Sik; Lee, Deok Hyun; Han, Jung Ho; Shim, Hee Sang

2013-11-01

Denting is a phenomenon that a steam generator tube is distorted by a volume expansion of corrosion products of the tube support and tubesheet materials adjacent to the tube. Although denting has been mitigated by a modification of the design and material of the tube support structures, it has been an inevitable concern in the crevice region of the top of tubesheet. This paper provides a new technology to prevent denting by cladding the secondary surface of the tubesheet with a corrosion resistant material. In this study, Alloy 690 material was cladded onto the surface of an SA508 tubesheet to a thickness of about 9 mm. The corrosion rates of the original SA508 tubesheet and the Alloy 690 clad material were measured in acidic and alkaline simulated environments. Using Alloy 690 cladding, the corrosion rate of the tubesheet within a magnetite sludge pile decreased by a factor of 680 in 0.1 M NiCl2 solution at 300 °C, and by a factor of 58 in 2 M NaOH solution at 315 °C. This means that denting can drastically be prevented by cladding the secondary tubesheet surface with corrosion resistant materials.

Fourier transform infrared spectroscopic studies of the secondary structure and thermal denaturation of CaATPase from rabbit skeletal muscle

NASA Astrophysics Data System (ADS)

Jaworsky, Mark; Brauner, Joseph W.; Mendelsohn, Richard

Fourier transform i.r. spectroscopy has been used to monitor structural alterations induced by thermal denaturation of the intrinsic membrane protein CaATPase in aqueous media. The protein has been isolated, purified and studied in five forms: (i) In its native lipid environment after isolation from rabbit sarcoplasmic reticulum, both in H 2O and D 2O suspensions. (ii) After both mild and extensive tryptic digestion has cleaved those residues external to the membrane bilayer. (iii) Reconstituted in vesicle form with bovine brain sphingomyelin. Fourier deconvolution techniques have been used to enhance the resolution of the intrinsically overlapped Amide I and Amide II spectral regions. Large spectral alterations apparent in the deconvoluted spectra occur in these regions upon thermal denaturation of the protein which are consistent with the formation of a large proportion of β-antiparallel sheet form. The alteration parallels the loss in ATPase activity. A mild tryptic digestion increases slightly the proportion of α-helix and/or random coil secondary structure. A thermal transition to a form containing a high proportion of β structure is still evident. Extensive tryptic digestion nearly abolishes the alpha helical plus random coil secondary structure, while producing a high proportion of β form which is resistant to further thermally induced structural alterations. Studies of CaATPase reconstituted into vesicles with bovine brain sphingomyelin reveal a higher proportion of β structure than the native enzyme, with further introduction of β structure on thermal denaturation. Both the utility of deconvolution techniques and the necessity for caution in their application are apparent from the current experiments.

The Role of Proanthocyanidins Complex in Structure and Nutrition Interaction in Alfalfa Forage

PubMed Central

Jonker, Arjan; Yu, Peiqiang

2016-01-01

Alfalfa (Medicago sativa L.) is one of the main forages grown in the world. Alfalfa is a winter hardy, drought tolerant, N-fixing legume with a good longevity, high yield, high nutrient levels, high digestibility, unique structural to non-structural components ratio, high dry matter intake, and high animal productivity per hectare. However, its main limitation is its excessively rapid initial rate of protein degradation in the rumen, which results in pasture bloat and inefficient use of protein with consequent excessive excretions of nitrogen into the environment. Proanthocyanidins are secondary plant metabolites that can bind with protein and thereby reduce the rate and extent of ruminal protein degradation. However, these secondary metabolites do not accumulate in alfalfa. This review aims to firstly describe the events involved in the rapid release of protein from alfalfa and its effect on ruminant nutrition, environmental pollution, and pasture bloat; secondly, to describe occurrence, structure, functions and benefits of moderate amounts of proanthocyanidin; and finally, to describe the development of alfalfa which accumulates moderate amounts of proanthocyanidins. The emphasis of this review focuses on the role of proanthocyanidins compounds in structure and nutrition interaction in ruminant livestock systems. PMID:27223279

The Role of Proanthocyanidins Complex in Structure and Nutrition Interaction in Alfalfa Forage.

PubMed

Jonker, Arjan; Yu, Peiqiang

2016-05-23

Alfalfa (Medicago sativa L.) is one of the main forages grown in the world. Alfalfa is a winter hardy, drought tolerant, N-fixing legume with a good longevity, high yield, high nutrient levels, high digestibility, unique structural to non-structural components ratio, high dry matter intake, and high animal productivity per hectare. However, its main limitation is its excessively rapid initial rate of protein degradation in the rumen, which results in pasture bloat and inefficient use of protein with consequent excessive excretions of nitrogen into the environment. Proanthocyanidins are secondary plant metabolites that can bind with protein and thereby reduce the rate and extent of ruminal protein degradation. However, these secondary metabolites do not accumulate in alfalfa. This review aims to firstly describe the events involved in the rapid release of protein from alfalfa and its effect on ruminant nutrition, environmental pollution, and pasture bloat; secondly, to describe occurrence, structure, functions and benefits of moderate amounts of proanthocyanidin; and finally, to describe the development of alfalfa which accumulates moderate amounts of proanthocyanidins. The emphasis of this review focuses on the role of proanthocyanidins compounds in structure and nutrition interaction in ruminant livestock systems.

Idea Generating among Secondary School Teachers.

ERIC Educational Resources Information Center

Tomic, Welko; Brouwers, Andre

This study investigated where and how secondary school teachers generated ideas linked to their work environment. A group of 146 teachers from 20 secondary schools in the Netherlands completed an adapted version of Geschka's questionnaire, which focused on (1) teachers' preferred conditions, environments, media, people, and activities before the…

K-Partite RNA Secondary Structures

NASA Astrophysics Data System (ADS)

Jiang, Minghui; Tejada, Pedro J.; Lasisi, Ramoni O.; Cheng, Shanhong; Fechser, D. Scott

RNA secondary structure prediction is a fundamental problem in structural bioinformatics. The prediction problem is difficult because RNA secondary structures may contain pseudoknots formed by crossing base pairs. We introduce k-partite secondary structures as a simple classification of RNA secondary structures with pseudoknots. An RNA secondary structure is k-partite if it is the union of k pseudoknot-free sub-structures. Most known RNA secondary structures are either bipartite or tripartite. We show that there exists a constant number k such that any secondary structure can be modified into a k-partite secondary structure with approximately the same free energy. This offers a partial explanation of the prevalence of k-partite secondary structures with small k. We give a complete characterization of the computational complexities of recognizing k-partite secondary structures for all k ≥ 2, and show that this recognition problem is essentially the same as the k-colorability problem on circle graphs. We present two simple heuristics, iterated peeling and first-fit packing, for finding k-partite RNA secondary structures. For maximizing the number of base pair stackings, our iterated peeling heuristic achieves a constant approximation ratio of at most k for 2 ≤ k ≤ 5, and at most frac6{1-(1-6/k)^k} le frac6{1-e^{-6}} < 6.01491 for k ≥ 6. Experiment on sequences from PseudoBase shows that our first-fit packing heuristic outperforms the leading method HotKnots in predicting RNA secondary structures with pseudoknots. Source code, data set, and experimental results are available at http://www.cs.usu.edu/ mjiang/rna/kpartite/.

Do family and neighbourhood matter in secondary school completion? A multilevel study of determinants and their interactions in a life-course perspective.

PubMed

Myhr, Arnhild; Lillefjell, Monica; Espnes, Geir Arild; Halvorsen, Thomas

2017-01-01

Completion of secondary education is important for individuals' future health and health behaviour. The fundamental purpose of this study is to investigate the variation and clustering of school completion in families and neighbourhoods. Secondly, we aim to examine the impact of individuals' family structure and neighbourhood of residence and examine to what extent parental education level moderates these associations. Longitudinal register data for 30% of the entire Norwegian population aged 21-27 years in 2010 (N = 107,003) was extracted from Statistic Norway´s event database. Three-level logistic regression models, which incorporated individual, family, and neighbourhood contextual factors, were applied to estimate the family and neighbourhood general contextual effects and detect possible educational differences in the impact of family structure and urban place of residence in school completion. Completion rates were significantly higher within families with higher education level (79% in tertiary educated families vs. 61% and 48% in secondary and primary educated families respectively) and were strongly correlated within families (ICC = 39.6) and neighbourhoods (ICC = 5.7). Several structural factors at the family level negatively associated with school completion (e.g., family disruption, large family size, and young maternal age) were more prevalent and displayed more negative impact among primary educated individuals. Urban residence was associated with school completion, but only among the tertiary educated. Investment in the resources in the individuals' immediate surroundings, including family and neighbourhood, may address a substantial portion of the social inequalities in the completion of upper secondary education. The high intra-familial correlation in school completion suggests that public health policies and future research should acknowledge family environments in order to improve secondary education completion rates among young people within lower educated families.

Structures of the E46K Mutant-Type α-Synuclein Protein and Impact of E46K Mutation on the Structures of the Wild-Type α-Synuclein Protein

PubMed Central

2013-01-01

The E46K genetic missense mutation of the wild-type α-synuclein protein was recently identified in a family of Spanish origin with hereditary Parkinson’s disease. Detailed understanding of the structures of the monomeric E46K mutant-type α-synuclein protein as well as the impact of the E46K missense mutation on the conformations and free energy landscapes of the wild-type α-synuclein are required for gaining insights into the pathogenic mechanism of Parkinson’s disease. In this study, we use extensive parallel tempering molecular dynamics simulations along with thermodynamic calculations to assess the secondary and tertiary structural properties as well as the conformational preferences of the monomeric wild-type and E46K mutant-type α-synuclein proteins in an aqueous solution environment. We also present the residual secondary structure component conversion stabilities with dynamics using a theoretical strategy, which we most recently developed. To the best of our knowledge, this study presents the first detailed comparison of the structural and thermodynamic properties of the wild-type and E46K mutant-type α-synuclein proteins in an aqueous solution environment at the atomic level with dynamics. We find that the E46K mutation results not only in local but also in long-range changes in the structural properties of the wild-type α-synuclein protein. The mutation site shows a significant decrease in helical content as well as a large increase in β-sheet structure formation upon E46K mutation. In addition, the β-sheet content of the C-terminal region increases significantly in the E46K mutant-type αS in comparison to the wild-type αS. Our theoretical strategy developed to assess the thermodynamic preference of secondary structure transitions indicates that this shift in secondary structure is the result of a decrease in the thermodynamic preference of turn to helix conversions while the coil to β-sheet preference increases for these residues. Long-range intramolecular protein interactions of the C-terminal with the N-terminal and NAC regions increase upon E46K mutation, resulting in more compact structures for the E46K mutant-type rather than wild-type αS. However, the E46K mutant-type αS structures are less stable than the wild-type αS. Overall, our results show that the E46K mutant-type αS has a higher propensity to aggregate than the wild-type αS and that the N-terminal and C-terminal regions are reactive toward fibrillization and aggregation upon E46K mutation and we explain the associated reasons based on the structural properties herein. Small molecules or drugs that can block the specific residues forming abundant β-sheet structure, which we report here, might help to reduce the reactivity of these intrinsically disordered fibrillogenic proteins toward aggregation and their toxicity. PMID:23374074

Associations between school-level environment and science classroom environment in secondary schools

NASA Astrophysics Data System (ADS)

Dorman, Jeffrey P.; Fraser, Barry J.; McRobbie, Campbell J.

1995-09-01

This article describes a study of links between school environment and science classroom environment. Instruments to assess seven dimensions of school environment (viz., Empowerment, Student Support, Affiliation, Professional Interest, Mission Consensus, Resource Adequacy and Work Pressure) and seven dimensions of classroom environment (viz., Student Affiliation, Interactions, Cooperation, Task Orientation, Order & Organisation, Individualisati n and Teacher Control) in secondary school science classrooms were developed and validated. The study involved a sample of 1,318 students in 64 year 9 and year 12 science classes and 128 teachers of science in Australian secondary schools. Using the class mean as the unit of analysis for student data, associations between school and classroom environment were investigated using simple, multiple and canonical correlational analyses. In general, results indicated weak relationships between school and classroom environments and they reinforced the view that characteristics of the school environment are not transmitted automatically into science classrooms.

Structural Technology and Analysis Program (STAP) Delivery Order 0004: Durability Patch

NASA Astrophysics Data System (ADS)

Ikegami, Roy; Haugse, Eric; Trego, Angela; Rogers, Lynn; Maly, Joe

2001-06-01

Structural cracks in secondary structure, resulting from a high cycle fatigue (HCF) environment, are often referred to as nuisance cracks. This type of damage can result in costly inspections and repair. The repairs often do not last long because the repaired structure continues to respond in a resonant fashion to the environment. Although the use of materials for passive damping applications is well understood, there are few applications to high-cycle fatigue problems. This is because design information characterization temperature, resonant response frequency and strain levels are difficult to determine. The Durability Patch and Damage Dosimeter Program addressed these problems by: (1) Developing a damped repair design process which includes a methodology for designing the material and application characteristics required to optimally damp the repair. (2) Designing and developing a rugged, small, and lightweight data acquisition unit called the damage dosimeter. This is a battery operated, single board computer, capable of collecting three channels of strain and one channel of temperature, processing this data by user developed algorithms written in the C programming language, and storing the processed data in resident memory. The dosimeter is used to provide flight data needed to characterize the vibration environment. The vibration environment is then used to design the damping material characteristics and repair. The repair design methodology and dosimeter were demonstrated on B-52, C-130, and F-15 aircraft applications.

On the interplay between cosmological shock waves and their environment

NASA Astrophysics Data System (ADS)

Martin-Alvarez, Sergio; Planelles, Susana; Quilis, Vicent

2017-05-01

Cosmological shock waves are tracers of the thermal history of the structures in the Universe. They play a crucial role in redistributing the energy within the cosmic structures and are also amongst the main ingredients of galaxy and galaxy cluster formation. Understanding this important function requires a proper description of the interplay between shocks and the different environments where they can be found. In this paper, an Adaptive Mesh Refinement (AMR) Eulerian cosmological simulation is analysed by means of a shock-finding algorithm that allows to generate shock wave maps. Based on the population of dark matter halos and on the distribution of density contrast in the simulation, we classify the shocks in five different environments. These range from galaxy clusters to voids. The shock distribution function and the shocks power spectrum are studied for these environments dynamics. We find that shock waves on different environments undergo different formation and evolution processes, showing as well different characteristics. We identify three different phases of formation, evolution and dissipation of these shock waves, and an intricate migration between distinct environments and scales. Shock waves initially form at external, low density regions and are merged and amplified through the collapse of structures. Shock waves and cosmic structures follow a parallel evolution. Later on, shocks start to detach from them and dissipate. We also find that most of the power that shock waves dissipate is found at scales of k ˜0.5 Mpc^{-1}, with a secondary peak at k ˜8 Mpc^{-1}. The evolution of the shocks power spectrum confirms that shock waves evolution is coupled and conditioned by their environment.

Clinical Supervision Skills: Managing the Clinical Environment. Health Occupations Clinical Teacher Education Series for Secondary and Post-Secondary Educators.

ERIC Educational Resources Information Center

Shea, Mary Lou; And Others

This learning module, which is part of a staff development program for health occupations clinical instructors, discusses the process of managing the physical clinical environment and students' experiences within the clinical environment. It includes learning activities dealing with various aspects of managing the physical environment and student…

Nuclear Radiation Fields on the Mars Surface: Risk Analysis for Long-term Living Environment

NASA Technical Reports Server (NTRS)

Anderson, Brooke M.; Clowdsley, Martha S.; Qualls, Garry D.; Nealy, John E.

2005-01-01

Mars, our nearest planet outward from the sun, has been targeted for several decades as a prospective site for expanded human habitation. Background space radiation exposures on Mars are expected to be orders of magnitude higher than on Earth. Recent risk analysis procedures based on detailed dosimetric techniques applicable to sensitive human organs have been developed along with experimental data regarding cell mutation rates resulting from exposures to a broad range of particle types and energy spectra. In this context, simulated exposure and subsequent risk for humans in residence on Mars are examined. A conceptual habitat structure, CAD-modeled with duly considered inherent shielding properties, has been implemented. Body self-shielding is evaluated using NASA standard computerized male and female models. The background environment is taken to consist not only of exposure from incident cosmic ray ions and their secondaries, but also include the contribution from secondary neutron fields produced in the tenuous atmosphere and the underlying regolith.

An Explorative Study on Environmental Literacy among the Secondary Level Students in Bangladesh

ERIC Educational Resources Information Center

Sarkar, Md. Mahbub Alam; Ara, Quazi Afroz Jahan; Raihan, Jahir; Ozaki, Koji

2008-01-01

This study was intended to explore the environmental literacy among the secondary level students of Bangladesh. Specifically, it was designed to: i) determine environmental knowledge of the secondary students, ii) explore their environmental attitude, iii) find out their environment related practices, and iv) explore school's environment-friendly…

Authentic leadership, empowerment and burnout: a comparison in new graduates and experienced nurses.

PubMed

Laschinger, Heather K Spence; Wong, Carol A; Grau, Ashley L

2013-04-01

To examine the effect of authentic leadership and structural empowerment on the emotional exhaustion and cynicism of new graduates and experienced acute-care nurses. Employee empowerment is a fundamental component of healthy work environments that promote nurse health and retention, and nursing leadership is key to creating these environments. In a secondary analysis of data from two studies we compared the pattern of relationships among study variables in two Ontario groups: 342 new graduates with <2 years of experience and 273 nurses with more than 2 years of experience. A multi-group path analysis using Structural Equation Modelling indicated an acceptable fit of the final model (χ(2) = 17.52, df = 2, P < 0.001, CFI = 0.97, IFI = 0.97 and RMSEA = 0.11). Authentic leadership significantly and negatively influenced emotional exhaustion and cynicism through workplace empowerment in both groups. The authentic behaviour of nursing leaders was important to nurses' perceptions of structurally empowering conditions in their work environments, regardless of experience level, and ultimately contributed to lower levels of emotional exhaustion and cynicism. Leadership training for nurse managers may help develop the empowering work environments required in today's health-care organizations in order to attract and retain nurses. © 2012 Blackwell Publishing Ltd.

Metabolome-genome-wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism

PubMed Central

Matsuda, Fumio; Nakabayashi, Ryo; Yang, Zhigang; Okazaki, Yozo; Yonemaru, Jun-ichi; Ebana, Kaworu; Yano, Masahiro; Saito, Kazuki

2015-01-01

Plants produce structurally diverse secondary (specialized) metabolites to increase their fitness for survival under adverse environments. Several bioactive compounds for new drugs have been identified through screening of plant extracts. In this study, genome-wide association studies (GWAS) were conducted to investigate the genetic architecture behind the natural variation of rice secondary metabolites. GWAS using the metabolome data of 175 rice accessions successfully identified 323 associations among 143 single nucleotide polymorphisms (SNPs) and 89 metabolites. The data analysis highlighted that levels of many metabolites are tightly associated with a small number of strong quantitative trait loci (QTLs). The tight association may be a mechanism generating strains with distinct metabolic composition through the crossing of two different strains. The results indicate that one plant species produces more diverse phytochemicals than previously expected, and plants still contain many useful compounds for human applications. PMID:25267402

Secondary Structure of Rat and Human Amylin across Force Fields

PubMed Central

Hoffmann, Kyle Quynn; McGovern, Michael; Chiu, Chi-cheng; de Pablo, Juan J.

2015-01-01

The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable dynamic pathways that facilitate the formation of aggregates and, eventually, amyloid fibrils. PMID:26221949

Secondary structure of rat and human amylin across force fields

DOE PAGES

Hoffmann, Kyle Quynn; McGovern, Michael; Chiu, Chi -cheng; ...

2015-07-29

The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin wasmore » determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable dynamic pathways that facilitate the formation of aggregates and, eventually, amyloid fibrils.« less

Radiation Environment Inside Spacecraft

NASA Technical Reports Server (NTRS)

O'Neill, Patrick

2015-01-01

Dr. Patrick O'Neill, NASA Johnson Space Center, will present a detailed description of the radiation environment inside spacecraft. The free space (outside) solar and galactic cosmic ray and trapped Van Allen belt proton spectra are significantly modified as these ions propagate through various thicknesses of spacecraft structure and shielding material. In addition to energy loss, secondary ions are created as the ions interact with the structure materials. Nuclear interaction codes (FLUKA, GEANT4, HZTRAN, MCNPX, CEM03, and PHITS) transport free space spectra through different thicknesses of various materials. These "inside" energy spectra are then converted to Linear Energy Transfer (LET) spectra and dose rate - that's what's needed by electronics systems designers. Model predictions are compared to radiation measurements made by instruments such as the Intra-Vehicular Charged Particle Directional Spectrometer (IV-CPDS) used inside the Space Station, Orion, and Space Shuttle.

The Development of a Survey Instrument to Measure Transactional Distance in Secondary Blended Learning Environments

ERIC Educational Resources Information Center

Lane, Dennis Glenn

2017-01-01

The goal of this study was to develop a survey instrument to measure transactional distance in secondary blended learning environments. This study resulted in a 35-item survey instrument, the Blended Learning Assessment Scale of Transactional Distance (BLASTD), which was tested using a convenience sample of secondary students (n = 222) at a…

The Constructivist Classroom Learning Environment and Its Associations with Critical Thinking Ability of Secondary School Students in Liberal Studies

ERIC Educational Resources Information Center

Kwan, Yee Wan; Wong, Angela F. L.

2014-01-01

In this study, we investigated-secondary school students' perceptions of their constructivist learning environment in Liberal Studies, and whether their perceptions were related to their critical thinking ability. A convenience sample of Secondary Three students (N = 967) studying Liberal Studies in Hong Kong participated in this research by…

Adolescent Alienation: The Effects of Disability, Gender, and Ethnicity on Perceptions of School Life in Secondary Environments

ERIC Educational Resources Information Center

Brown, Monica R.

2005-01-01

Responses to the School Factors Questionnaire (SFQ) administered to 222 students were used to ascertain student perceptions of alienating factors within secondary school environments. Descriptive statistics (i.e., frequency of responses to SFQ items) were used to report the data. The results indicated that although secondary students liked coming…

Drugs from the Oceans: Marine Natural Products as Leads for Drug Discovery.

PubMed

Altmann, Karl-Heinz

2017-10-25

The marine environment harbors a vast number of species that are the source of a wide array of structurally diverse bioactive secondary metabolites. At this point in time, roughly 27'000 marine natural products are known, of which eight are (were) at the origin of seven marketed drugs, mostly for the treatment of cancer. The majority of these drugs and also of drug candidates currently undergoing clinical evaluation (excluding antibody-drug conjugates) are unmodified natural products, but synthetic chemistry has played a central role in the discovery and/or development of all but one of the approved marine-derived drugs. More than 1000 new marine natural products have been isolated per year over the last decade, but the pool of new and unique structures is far from exhausted. To fully leverage the potential offered by the structural diversity of marine-produced secondary metabolites for drug discovery will require their broad assessment for different bioactivities and the productive interplay between new fermentation technologies, synthetic organic chemistry, and medicinal chemistry, in order to secure compound supply and enable lead optimization.

Changes in secondary structure of gluten proteins due to emulsifiers

NASA Astrophysics Data System (ADS)

Gómez, Analía V.; Ferrer, Evelina G.; Añón, María C.; Puppo, María C.

2013-02-01

Changes in the secondary structure of gluten proteins due to emulsifiers were analyzed by Raman Spectroscopy. The protein folding induced by 0.25% SSL (Sodium Stearoyl Lactylate) (GS0.25, Gluten + 0.25% SSL) included an increase in α-helix conformation and a decrease in β-sheet, turns and random coil. The same behavior, although in a less degree, was observed for 0.5% gluten-DATEM (Diacetyl Tartaric Acid Esters of Monoglycerides) system. The low burial of Tryptophan residues to a more hydrophobic environment and the low percentage area of the C-H stretching band for GS0.25 (Gluten + 0.25% SSL), could be related to the increased in α-helix conformation. This behavior was also confirmed by changes in stretching vibrational modes of disulfide bridges (S-S) and the low exposure of Tyrosine residues. High levels of SSL (0.5% and 1.0%) and DATEM (1.0%) led to more disordered protein structures, with different gluten networks. SSL (1.0%) formed a more disordered and opened gluten matrix than DATEM, the last one being laminar and homogeneous.

Novel Approach to Classify Plants Based on Metabolite-Content Similarity.

PubMed

Liu, Kang; Abdullah, Azian Azamimi; Huang, Ming; Nishioka, Takaaki; Altaf-Ul-Amin, Md; Kanaya, Shigehiko

2017-01-01

Secondary metabolites are bioactive substances with diverse chemical structures. Depending on the ecological environment within which they are living, higher plants use different combinations of secondary metabolites for adaptation (e.g., defense against attacks by herbivores or pathogenic microbes). This suggests that the similarity in metabolite content is applicable to assess phylogenic similarity of higher plants. However, such a chemical taxonomic approach has limitations of incomplete metabolomics data. We propose an approach for successfully classifying 216 plants based on their known incomplete metabolite content. Structurally similar metabolites have been clustered using the network clustering algorithm DPClus. Plants have been represented as binary vectors, implying relations with structurally similar metabolite groups, and classified using Ward's method of hierarchical clustering. Despite incomplete data, the resulting plant clusters are consistent with the known evolutional relations of plants. This finding reveals the significance of metabolite content as a taxonomic marker. We also discuss the predictive power of metabolite content in exploring nutritional and medicinal properties in plants. As a byproduct of our analysis, we could predict some currently unknown species-metabolite relations.

Novel Approach to Classify Plants Based on Metabolite-Content Similarity

PubMed Central

Abdullah, Azian Azamimi; Huang, Ming; Nishioka, Takaaki

2017-01-01

Secondary metabolites are bioactive substances with diverse chemical structures. Depending on the ecological environment within which they are living, higher plants use different combinations of secondary metabolites for adaptation (e.g., defense against attacks by herbivores or pathogenic microbes). This suggests that the similarity in metabolite content is applicable to assess phylogenic similarity of higher plants. However, such a chemical taxonomic approach has limitations of incomplete metabolomics data. We propose an approach for successfully classifying 216 plants based on their known incomplete metabolite content. Structurally similar metabolites have been clustered using the network clustering algorithm DPClus. Plants have been represented as binary vectors, implying relations with structurally similar metabolite groups, and classified using Ward's method of hierarchical clustering. Despite incomplete data, the resulting plant clusters are consistent with the known evolutional relations of plants. This finding reveals the significance of metabolite content as a taxonomic marker. We also discuss the predictive power of metabolite content in exploring nutritional and medicinal properties in plants. As a byproduct of our analysis, we could predict some currently unknown species-metabolite relations. PMID:28164123

Unpacking socio-economic risks for reading and academic self-concept in primary school: Differential effects and the role of the preschool home learning environment.

PubMed

Crampton, Alexandria; Hall, James

2017-09-01

Uncertainty remains concerning how children's reading and academic self-concept are related and how these are differentially affected by social disadvantage and home learning environments. To contrast the impacts of early socio-economic risks and preschool home learning environments upon British children's reading abilities and academic self-concept between 7 and 10 years. n = 3,172 British children aged 3-10 years and their families. A secondary analysis of the nationally representative UK EPPE database. Multilevel structural equation modelling calculated the direct, indirect, and total impacts of early socio-economic risks (0-3 years) and preschool home learning environments (3-5 years) upon children's reading ability and academic self-concept between 7 and 10 years. Early socio-economic risk had different effects upon children's reading ability and academic self-concept. Early socio-economic risks affected children's reading at ages 7 and 10 both directly and indirectly via effects upon preschool home learning environments. By contrast, early socio-economic risks had only indirect effects upon children's academic self-concept via less stimulating home learning environments in the preschool period and by limiting reading abilities early on in primary school. Although the impacts of early socio-economic risks are larger and more easily observed upon reading than upon academic self-concept, they can impact both by making it less likely that children will experience enriching home learning environments during the preschool period. This has implications for social policymakers, early educators, and interventionists. Intervening early and improving preschool home learning environments can do more than raise children's reading abilities; secondary benefits may also be achievable upon children's self-concept. © 2017 The British Psychological Society.

CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts

PubMed Central

Hafsa, Noor E.; Arndt, David; Wishart, David S.

2015-01-01

The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I′, II′ and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. PMID:25979265

The structure of the CD3 ζζ transmembrane dimer in POPC and raft-like lipid bilayer: a molecular dynamics study.

PubMed

Petruk, Ariel Alcides; Varriale, Sonia; Coscia, Maria Rosaria; Mazzarella, Lelio; Merlino, Antonello; Oreste, Umberto

2013-11-01

Plasma membrane lipids significantly affect assembly and activity of many signaling networks. The present work is aimed at analyzing, by molecular dynamics simulations, the structure and dynamics of the CD3 ζζ dimer in palmitoyl-oleoyl-phosphatidylcholine bilayer (POPC) and in POPC/cholesterol/sphingomyelin bilayer, which resembles the raft membrane microdomain supposed to be the site of the signal transducing machinery. Both POPC and raft-like environment produce significant alterations in structure and flexibility of the CD3 ζζ with respect to nuclear magnetic resonance (NMR) model: the dimer is more compact, its secondary structure is slightly less ordered, the arrangement of the Asp6 pair, which is important for binding to the Arg residue in the alpha chain of the T cell receptor (TCR), is stabilized by water molecules. Different interactions of charged residues with lipids at the lipid-cytoplasm boundary occur when the two environments are compared. Furthermore, in contrast to what is observed in POPC, in the raft-like environment correlated motions between transmembrane and cytoplasmic regions are observed. Altogether the data suggest that when the TCR complex resides in the raft domains, the CD3 ζζ dimer assumes a specific conformation probably necessary to the correct signal transduction. © 2013.

Secondary Traumatic Stress and Burnout of North Korean Refugees Service Providers

PubMed Central

2017-01-01

Objective The current study investigated the burnout and secondary traumatic stress of service providers for North Korean (NK) refugees based on the conceptual framework of theJob Demands-Resources (JD-R) model of workplace burnout. Methods A cross-sectional self-administered survey was conducted with a national sample consisting of all 63 organizations in direct services to North Korean refugees. Of the estimated total number of 230 service providers comprising of social workers, psychotherapists, job counselors and paraprofessional counselors, 179 completed the survey, a 77.8% return rate. Results While job resources such as personal commitment to work and organizational support indicated inverse relations to burnout, job demands such as workload, work environment and secondary traumatic stress (STS) showed a positive relationship to worker burnout. The STS were present in more than half of the respondents (51.3%), of which 20.7% of them indicating a severe level of STS. The STS proved to be the most significant risk to worker burnout as it showed strong relations to all three dimensions of burnout. Conclusion Structural issues of chronic work overload and poor work environment need to be addressed to reduce staff burnout. STS is a serious occupational hazard in working with North Korean refugees. PMID:28326108

Molecular marker to identify radiolarian species -toward establishment of paleo-environmental proxy-

NASA Astrophysics Data System (ADS)

Ishitani, Y.

2017-12-01

Marine fossilized unicellular plankton are known to have many genetically divergent species (biological species) in the single morphological species and these biological species show the species-specific environments much more precisely than that of morphological species. Among these plankton, Radiolaria are one of the best candidates for time- and environmental-indicators in the modern and past oceans, because radiolarians are the only group which represent entire water column from shallow to deep waters. However, the ecology and evolution of radiolarian were traditionally studied in paleontology and paleoceanography by morphological species. Even Radiolaria has a huge potential for novel proxy of wide and deep environments, there is no criterion to identify the biological species. The motivation for this study is setting the quantitative delimitation to establish the biological species of radiolarians based on molecular data, for leading the future ecological and paleo-environmental study. Identification of the biological species by ribosomal DNA sequences are mainly based on two ways: one is the evolutionary distance of the small subunit (SSU) rDNA, the internal transcribed spacer region of ribosomal DNA (ITS1 and 2), and the large subunit (LSU) rDNA; and the other is the secondary structure of ITS2. In the present study, all four possible genetic markers (SSU, ITS1, ITS2, and LSU rDNA) were amplified from 232 individuals of five radiolarian morphological species and applied to examine the evolutionary distance and secondary structure of rDNA. Comprehensive survey clearly shows that evolutionary distance of ITS1 rDNA and the secondary structure of ITS2 is good to identify the species. Notably, evolutionary distance of ITS1 rDNA is possible to set the common delimitation to identify the biological species, as 0.225 substitution per site. The results show that the ITS1 and ITS 2 rDNA could be the criterion for radiolarian species identification.

40 CFR 421.320 - Applicability: Description of the secondary uranium subcategory.

Code of Federal Regulations, 2012 CFR

2012-07-01

... secondary uranium subcategory. 421.320 Section 421.320 Protection of Environment ENVIRONMENTAL PROTECTION... CATEGORY Secondary Uranium Subcategory § 421.320 Applicability: Description of the secondary uranium... uranium (including depleted uranium) by secondary uranium facilities. ...

40 CFR 421.320 - Applicability: Description of the secondary uranium subcategory.

Code of Federal Regulations, 2011 CFR

2011-07-01

... secondary uranium subcategory. 421.320 Section 421.320 Protection of Environment ENVIRONMENTAL PROTECTION... CATEGORY Secondary Uranium Subcategory § 421.320 Applicability: Description of the secondary uranium... uranium (including depleted uranium) by secondary uranium facilities. ...

40 CFR 421.320 - Applicability: Description of the secondary uranium subcategory.

Code of Federal Regulations, 2013 CFR

2013-07-01

... secondary uranium subcategory. 421.320 Section 421.320 Protection of Environment ENVIRONMENTAL PROTECTION... CATEGORY Secondary Uranium Subcategory § 421.320 Applicability: Description of the secondary uranium... uranium (including depleted uranium) by secondary uranium facilities. ...

40 CFR 421.320 - Applicability: Description of the secondary uranium subcategory.

Code of Federal Regulations, 2014 CFR

2014-07-01

... secondary uranium subcategory. 421.320 Section 421.320 Protection of Environment ENVIRONMENTAL PROTECTION... CATEGORY Secondary Uranium Subcategory § 421.320 Applicability: Description of the secondary uranium... uranium (including depleted uranium) by secondary uranium facilities. ...

40 CFR 421.320 - Applicability: Description of the secondary uranium subcategory.

Code of Federal Regulations, 2010 CFR

2010-07-01

... secondary uranium subcategory. 421.320 Section 421.320 Protection of Environment ENVIRONMENTAL PROTECTION... CATEGORY Secondary Uranium Subcategory § 421.320 Applicability: Description of the secondary uranium... uranium (including depleted uranium) by secondary uranium facilities. ...

Science Laboratory Learning Environments in Junior Secondary Schools

ERIC Educational Resources Information Center

Kwok, Ping Wai

2015-01-01

A Chinese version of the Science Laboratory Environment Inventory (SLEI) was used to study the students' perceptions of the actual and preferred laboratory learning environments in Hong Kong junior secondary science lessons. Valid responses of the SLEI from 1932 students of grade 7 to grade 9 indicated that an open-ended inquiry approach seldom…

A Structural Equation Model (SEM) of the Impact of Transformational, Visionary, Charismatic and Ethical Leadership Styles on the Development of Wise Leadership among Filipino Private Secondary School Principals

ERIC Educational Resources Information Center

Parco-Tropicales, Marishirl; de Guzman, Allan B.

2014-01-01

In recent years, wisdom is seen as a key resource for school leaders in dealing with the dynamics of the changing school environments. This study purports to expand the growing interest on wisdom by testing a model that describes the impact of transformational, visionary, charismatic and ethical leadership styles on wise leadership development…

Structural perturbations on huntingtin N17 domain during its folding on 2D-nanomaterials

NASA Astrophysics Data System (ADS)

Zhang, Leili; Feng, Mei; Zhou, Ruhong; Luan, Binquan

2017-09-01

A globular protein’s folded structure in its physiological environment is largely determined by its amino acid sequence. Recently, newly discovered transformer proteins as well as intrinsically disordered proteins may adopt the folding-upon-binding mechanism where their secondary structures are highly dependent on their binding partners. Due to the various applications of nanomaterials in biological sensors and potential wearable devices, it is important to discover possible conformational changes of proteins on nanomaterials. Here, through molecular dynamics simulations, we show that the first 17 residues of the huntingtin protein (HTT-N17) exhibit appreciable differences during its folding on 2D-nanomaterials, such as graphene and MoS2 nanosheets. Namely, the protein is disordered on the graphene surface but is helical on the MoS2 surface. Despite that the amphiphilic environment at the nanosheet-water interface promotes the folding of the amphipathic proteins (such as HTT-N17), competitions between protein-nanosheet and intra-protein interactions yield very different protein conformations. Therefore, as engineered binding partners, nanomaterials might significantly affect the structures of adsorbed proteins.

High School STEM Teachers' Perceptions of the Work Environment

ERIC Educational Resources Information Center

Pedersen, Daphne E.; West, Robert R.

2017-01-01

How do secondary STEM teachers perceive the environments in which they teach? To what degree is STEM teaching at the secondary level situated in a gendered workplace organization? Using data from the 1999-2000 Schools and Staffing Survey, we examined how men and women who were full-time secondary school teachers in STEM fields (N = 5,617)…

Influence of School Environment on the Management of Secondary School Education in Makurdi Metropolis of Benue State, Nigeria

ERIC Educational Resources Information Center

Bua, Felix Terhile

2013-01-01

The study investigated the influence of school environment on the management of secondary school education in Makurdi Metropolis of Benue State. Two research questions and two hypotheses guided the study. The survey design was adopted for the study. Four hundred (400) teachers from 20 grant aided secondary schools in Markurdi Metropolis of Benue…

Adolescents' Perception of the Psychological Security of School Environment, Emotional Development and Academic Performance in Secondary Schools in Gombe Metropolis

ERIC Educational Resources Information Center

Musa, Alice K. J.; Meshak, Bibi; Sagir, Jummai Ibrahim

2016-01-01

The purpose of the study was to determine adolescents' perceptions of the psychological security of their schools environments and their relationship with their emotional development and academic performance in secondary schools in Gombe Metropolis. A sample of 239 (107 males and 133 females) secondary school students selected via stratified…

40 CFR Table 2 to Subpart X of... - Emissions Limits for Secondary Lead Smelting Furnaces

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 10 2014-07-01 2014-07-01 false Emissions Limits for Secondary Lead Smelting Furnaces 2 Table 2 to Subpart X of Part 63 Protection of Environment ENVIRONMENTAL PROTECTION... Pt. 63, Subpt. X, Table 2 Table 2 to Subpart X of Part 63—Emissions Limits for Secondary Lead...

40 CFR Table 2 to Subpart X of... - Emissions Limits for Secondary Lead Smelting Furnaces

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 10 2013-07-01 2013-07-01 false Emissions Limits for Secondary Lead Smelting Furnaces 2 Table 2 to Subpart X of Part 63 Protection of Environment ENVIRONMENTAL PROTECTION... Pt. 63, Subpt. X, Table 2 Table 2 to Subpart X of Part 63—Emissions Limits for Secondary Lead...

40 CFR Table 2 to Subpart X of... - Emissions Limits for Secondary Lead Smelting Furnaces

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 10 2012-07-01 2012-07-01 false Emissions Limits for Secondary Lead Smelting Furnaces 2 Table 2 to Subpart X of Part 63 Protection of Environment ENVIRONMENTAL PROTECTION... Pt. 63, Subpt. X, Table 2 Table 2 to Subpart X of Part 63—Emissions Limits for Secondary Lead...

CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.

PubMed

Hafsa, Noor E; Arndt, David; Wishart, David S

2015-07-01

The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I', II' and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

The conservation and function of RNA secondary structure in plants

PubMed Central

Vandivier, Lee E.; Anderson, Stephen J.; Foley, Shawn W.; Gregory, Brian D.

2016-01-01

RNA transcripts fold into secondary structures via intricate patterns of base pairing. These secondary structures impart catalytic, ligand binding, and scaffolding functions to a wide array of RNAs, forming a critical node of biological regulation. Among their many functions, RNA structural elements modulate epigenetic marks, alter mRNA stability and translation, regulate alternative splicing, transduce signals, and scaffold large macromolecular complexes. Thus, the study of RNA secondary structure is critical to understanding the function and regulation of RNA transcripts. Here, we review the origins, form, and function of RNA secondary structure, focusing on plants. We then provide an overview of methods for probing secondary structure, from physical methods such as X-ray crystallography and nuclear magnetic resonance imaging (NMR) to chemical and nuclease probing methods. Marriage with high-throughput sequencing has enabled these latter methods to scale across whole transcriptomes, yielding tremendous new insights into the form and function of RNA secondary structure. PMID:26865341

JNSViewer—A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures

PubMed Central

Dong, Min; Graham, Mitchell; Yadav, Nehul

2017-01-01

Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and interactive correspondence among nucleotides, dot-bracket data, secondary structure graphs, and genic annotations. In JNSViewer, users can perform RNA secondary structure predictions with different programs and settings, add customized genic annotations in GFF format to structure graphs, search for specific linear motifs, and extract relevant structure graphs of sub-sequences. JNSViewer also allows users to choose a transcript or specific segment of Arabidopsis thaliana genome sequences and predict the corresponding secondary structure. Popular genome browsers (i.e., JBrowse and BrowserGenome) were integrated into JNSViewer to provide powerful visualizations of chromosomal locations, genic annotations, and secondary structures. In addition, we used StructureFold with default settings to predict some RNA structures for Arabidopsis by incorporating in vivo high-throughput RNA structure profiling data and stored the results in our web server, which might be a useful resource for RNA secondary structure studies in plants. JNSViewer is available at http://bioinfolab.miamioh.edu/jnsviewer/index.html. PMID:28582416

Bioactive Secondary Metabolites from a Thai Collection of Soil and Marine-Derived Fungi of the Genera Neosartorya and Aspergillus.

PubMed

Zin, War War May; Prompanya, Chadaporn; Buttachon, Suradet; Kijjoa, Anake

2016-01-01

Fungi are microorganisms which can produce interesting secondary metabolites with structural diversity. Although terrestrial fungi have been extensively investigated for their bioactive secondary metabolites such as antibiotics, marine-derived fungi have only recently attracted attention of Natural Products chemists. Our group has been working on the secondary metabolites produced by the cultures of the fungi of the genera Neosartorya and Aspergillus, collected from soil and marine environments from the tropical region for the purpose of finding new leads for anticancer and antibacterial drugs. This review covers only the secondary metabolites of four soil and six marine-derived species of Neosarorya as well as a new species of marine-derived Aspergillus, investigated by our group. In total, we have isolated fifty three secondary metabolites which can be categorized as polyketides (two), isocoumarins (six), terpenoids (two), meroterpenes (fourteen), alkaloids (twenty eight) and cyclic peptide (one). The anticancer and antibacterial activities of these fungal metabolites are also discussed. Among fifty three secondary metabolites isolated, only the alkaloid eurochevalierine and the cadinene sesquiterpene, isolated from the soil fungus N. pseudofisheri, showed relevant in vitro cytostatic activity against glioblastoma (U373) and non-small cell lung cancer (A549) cell lines while the meroditerpene aszonapyrone A exhibited strong antibacterial activity against multidrug-resistant Gram-positive bacteria and also strong antibiofilm activity in these isolates.

Martian Neutron Energy Spectrometer (MANES)

NASA Technical Reports Server (NTRS)

Maurer, R. H.; Roth, D. R.; Kinnison, J. D.; Goldsten, J. O.; Fainchtein, R.; Badhwar, G.

2000-01-01

High energy charged particles of extragalactic, galactic, and solar origin collide with spacecraft structures and planetary atmospheres. These primaries create a number of secondary particles inside the structures or on the surfaces of planets to produce a significant radiation environment. This radiation is a threat to long term inhabitants and travelers for interplanetary missions and produces an increased risk of carcinogenesis, central nervous system (CNS) and DNA damage. Charged particles are readily detected; but, neutrons, being electrically neutral, are much more difficult to monitor. These secondary neutrons are reported to contribute 30-60% of the dose equivalent in the Shuttle and MIR station. The Martian atmosphere has an areal density of 37 g/sq cm primarily of carbon dioxide molecules. This shallow atmosphere presents fewer mean free paths to the bombarding cosmic rays and solar particles. The secondary neutrons present at the surface of Mars will have undergone fewer generations of collisions and have higher energies than at sea level on Earth. Albedo neutrons produced by collisions with the Martian surface material will also contribute to the radiation environment. The increased threat of radiation damage to humans on Mars occurs when neutrons of higher mean energy traverse the thin, dry Martian atmosphere and encounter water in the astronaut's body. Water, being hydrogeneous, efficiently moderates the high energy neutrons thereby slowing them as they penetrate deeply into the body. Consequently, greater radiation doses can be deposited in or near critical organs such as the liver or spleen than is the case on Earth. A second significant threat is the possibility of a high energy heavy ion or neutron causing a DNA double strand break in a single strike.

Rtools: a web server for various secondary structural analyses on single RNA sequences.

PubMed

Hamada, Michiaki; Ono, Yukiteru; Kiryu, Hisanori; Sato, Kengo; Kato, Yuki; Fukunaga, Tsukasa; Mori, Ryota; Asai, Kiyoshi

2016-07-08

The secondary structures, as well as the nucleotide sequences, are the important features of RNA molecules to characterize their functions. According to the thermodynamic model, however, the probability of any secondary structure is very small. As a consequence, any tool to predict the secondary structures of RNAs has limited accuracy. On the other hand, there are a few tools to compensate the imperfect predictions by calculating and visualizing the secondary structural information from RNA sequences. It is desirable to obtain the rich information from those tools through a friendly interface. We implemented a web server of the tools to predict secondary structures and to calculate various structural features based on the energy models of secondary structures. By just giving an RNA sequence to the web server, the user can get the different types of solutions of the secondary structures, the marginal probabilities such as base-paring probabilities, loop probabilities and accessibilities of the local bases, the energy changes by arbitrary base mutations as well as the measures for validations of the predicted secondary structures. The web server is available at http://rtools.cbrc.jp, which integrates software tools, CentroidFold, CentroidHomfold, IPKnot, CapR, Raccess, Rchange and RintD. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Predicting Students' Homework Environment Management at the Secondary School Level

ERIC Educational Resources Information Center

Xu, Jianzhong

2012-01-01

The present study examined empirical models of variables posited to predict students' homework environment management at the secondary school level. The participants were 866 8th graders from 61 classes and 745 11th graders from 46 classes. Most of the variance in homework environment management occurred at the student level, with classmates'…

Classroom Learning Environment and Motivation towards Mathematics among Secondary School Students in Uganda

ERIC Educational Resources Information Center

Opolot-Okurut, Charles

2010-01-01

This article reports a study of secondary students' perceptions of mathematics classroom learning environment and their associations with their motivation towards mathematics. A sample of 81 students (19 male and 62 female) in two schools were used. Student perceptions of the classroom environment were assessed using a modified What Is Happening…

The Provision of a Health Promoting Environment for HIV/AIDS Education: The Case of Namibian Senior Secondary Schools

ERIC Educational Resources Information Center

Campbell, Bob; Lubben, Fred

2003-01-01

HIV/AIDS programmes in schools ultimately intend to decrease high risk sexual behaviour. One factor facilitating this outcome is a strong health promoting environment in the school. This paper reports a study surveying the health promoting environments supporting HIV/AIDS education in Namibian senior secondary schools. It develops a…

The Effect of Simulation-Games Environment on Students' Achievement in and Attitudes to Mathematics in Secondary Schools

ERIC Educational Resources Information Center

Akinsola, M. K.; Animasahun, I. A.

2007-01-01

This study sought to determine the effect of simulation-games environment on students' achievement in attitudes to mathematics in secondary school. Data was collected from a sample of 147 students in senior secondary school in Osun-State, Nigeria. t-test and analysis of variance was used to analyze the data collected for the study. The finding…

The Effect of Simulation-Games Environment on Students Achievement in and Attitudes to Mathematics in Secondary Schools

ERIC Educational Resources Information Center

Akinsola, M. K.; Animasahun, I. A.

2007-01-01

This study sought to determine the effect of simulation-games environment on students' achievement in attitudes to mathematics in secondary school. Data was collected from a sample of 147 students in senior secondary school in Osun-State, Nigeria. t-test and analysis of variance was used to analyze the data collected for the study. The finding…

Sustainability of outdoor school ground smoking bans at secondary schools: a mixed-method study

PubMed Central

Rozema, A D; Mathijssen, J J P; Jansen, M W J; van Oers, J A M

2018-01-01

Abstract Background Although increasing numbers of countries are implementing outdoor school ground smoking bans at secondary schools, less attention is paid to the post-implementation period even though sustainability of a policy is essential for long-term effectiveness. Therefore, this study assesses the level of sustainability and examines perceived barriers/facilitators related to the sustainability of an outdoor school ground smoking ban at secondary schools. Methods A mixed-method design was used with a sequential explanatory approach. In phase I, 438 online surveys were conducted and in phase II, 15 semi-structured interviews were obtained from directors of relevant schools. ANOVA (phase I) and a thematic approach (phase II) were used to analyze data. Results Level of sustainability of an outdoor school ground smoking ban was high at the 48% Dutch schools with an outdoor smoking ban. Furthermore, school size was significantly associated with sustainability. The perceived barriers/facilitators fell into three categories: (i) smoking ban implementation factors (side-effects, enforcement, communication, guidelines and collaboration), (ii) school factors (physical environment, school culture, education type and school policy) and (iii) community environment factors (legislation and social environment). Conclusions Internationally, the spread of outdoor school ground smoking bans could be further promoted. Once implemented, the ban has become ‘normal’ practice and investments tend to endure. Moreover, involvement of all staff is important for sustainability as they function as role models, have an interrelationship with students, and share responsibility for enforcement. These findings are promising for the sustainability of future tobacco control initiatives to further protect against the morbidity/mortality associated with smoking. PMID:29016786

40 CFR 421.200 - Applicability: Description of the secondary mercury subcategory.

Code of Federal Regulations, 2010 CFR

2010-07-01

... secondary mercury subcategory. 421.200 Section 421.200 Protection of Environment ENVIRONMENTAL PROTECTION... CATEGORY Secondary Mercury Subcategory § 421.200 Applicability: Description of the secondary mercury... mercury from secondary mercury facilities processing recycled mercuric oxide batteries and other mercury...

40 CFR 421.200 - Applicability: Description of the secondary mercury subcategory.

Code of Federal Regulations, 2013 CFR

2013-07-01

... secondary mercury subcategory. 421.200 Section 421.200 Protection of Environment ENVIRONMENTAL PROTECTION... CATEGORY Secondary Mercury Subcategory § 421.200 Applicability: Description of the secondary mercury... mercury from secondary mercury facilities processing recycled mercuric oxide batteries and other mercury...

40 CFR 421.200 - Applicability: Description of the secondary mercury subcategory.

Code of Federal Regulations, 2011 CFR

2011-07-01

... secondary mercury subcategory. 421.200 Section 421.200 Protection of Environment ENVIRONMENTAL PROTECTION... CATEGORY Secondary Mercury Subcategory § 421.200 Applicability: Description of the secondary mercury... mercury from secondary mercury facilities processing recycled mercuric oxide batteries and other mercury...

40 CFR 421.200 - Applicability: Description of the secondary mercury subcategory.

Code of Federal Regulations, 2014 CFR

2014-07-01

... secondary mercury subcategory. 421.200 Section 421.200 Protection of Environment ENVIRONMENTAL PROTECTION... CATEGORY Secondary Mercury Subcategory § 421.200 Applicability: Description of the secondary mercury... mercury from secondary mercury facilities processing recycled mercuric oxide batteries and other mercury...

40 CFR 421.200 - Applicability: Description of the secondary mercury subcategory.

Code of Federal Regulations, 2012 CFR

2012-07-01

... secondary mercury subcategory. 421.200 Section 421.200 Protection of Environment ENVIRONMENTAL PROTECTION... CATEGORY Secondary Mercury Subcategory § 421.200 Applicability: Description of the secondary mercury... mercury from secondary mercury facilities processing recycled mercuric oxide batteries and other mercury...

Secondary eyewall formation as a progressive boundary layer response

NASA Astrophysics Data System (ADS)

Abarca, S. F.; Montgomery, M. T.; Bell, M. M.

2012-12-01

The robust observational (satellite based) evidence that secondary eyewalls are common features in major hurricanes contrasts with the scarce in situ observations of the phenomena and its life cycle. This lack of observations has resulted in an incomplete understanding of the dynamics of secondary eyewall formation (SEF). A wide variety of physical processes have been invoked to explain SEF, but only the recently proposed theory of a progressive boundary layer control in SEF has been supported by a variety of full physics mesoscale numerical integrations. The RAINEX field project provided unique observations of the secondary eyewall of Hurricane Rita (2005) both before and during the time Rita exhibited a clear secondary eyewall structure. These observations have contributed to the advancement of the understanding of the secondary eyewall phenomenon. However, in the RAINEX experiment, there was limited data sampling during the development of the secondary wind maxima, thereby precluding a complete observational investigation of the dynamics of SEF. In this presentation we adopt an azimuthally-averaged perspective of the flow dynamics and we test the newly proposed theory of a progressive boundary layer control on SEF. Specifically, we use both RAINEX data as well as data from high resolution, full physics mesoscale numerical simulations to initialize and force an axisymmetric slab boundary layer model with radial diffusion included. The objective is to investigate whether such a reduced boundary layer model can generate secondary wind maxima as a response to environments like those that result in SEF in nature and in full physics simulations.

Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures

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

Biedermannová, Lada, E-mail: lada.biedermannova@ibt.cas.cz; Schneider, Bohdan

2015-10-27

The hydration of protein crystal structures was studied at the level of individual amino acids. The dependence of the number of water molecules and their preferred spatial localization on various parameters, such as solvent accessibility, secondary structure and side-chain conformation, was determined. Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. Themore » results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon–donor hydrogen bonds, OH–π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.« less

Secure Secondary Use of Clinical Data with Cloud-based NLP Services. Towards a Highly Scalable Research Infrastructure.

PubMed

Christoph, J; Griebel, L; Leb, I; Engel, I; Köpcke, F; Toddenroth, D; Prokosch, H-U; Laufer, J; Marquardt, K; Sedlmayr, M

2015-01-01

The secondary use of clinical data provides large opportunities for clinical and translational research as well as quality assurance projects. For such purposes, it is necessary to provide a flexible and scalable infrastructure that is compliant with privacy requirements. The major goals of the cloud4health project are to define such an architecture, to implement a technical prototype that fulfills these requirements and to evaluate it with three use cases. The architecture provides components for multiple data provider sites such as hospitals to extract free text as well as structured data from local sources and de-identify such data for further anonymous or pseudonymous processing. Free text documentation is analyzed and transformed into structured information by text-mining services, which are provided within a cloud-computing environment. Thus, newly gained annotations can be integrated along with the already available structured data items and the resulting data sets can be uploaded to a central study portal for further analysis. Based on the architecture design, a prototype has been implemented and is under evaluation in three clinical use cases. Data from several hundred patients provided by a University Hospital and a private hospital chain have already been processed. Cloud4health has shown how existing components for secondary use of structured data can be complemented with text-mining in a privacy compliant manner. The cloud-computing paradigm allows a flexible and dynamically adaptable service provision that facilitates the adoption of services by data providers without own investments in respective hardware resources and software tools.

Summary of SLAC's SEY Measurement On Flat Accelerator Wall Materials

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

Le Pimpec, F.; /PSI, Villigen /SLAC

The electron cloud effect (ECE) causes beam instabilities in accelerator structures with intense positively charged bunched beams. Reduction of the secondary electron yield (SEY) of the beam pipe inner wall is effective in controlling cloud formation. We summarize SEY results obtained from flat TiN, TiZrV and Al surfaces carried out in a laboratory environment. SEY was measured after thermal conditioning, as well as after low energy, less than 300 eV, particle exposure.

Structures and Free Energy Landscapes of the Wild-Type and A30P Mutant-Type α-Synuclein Proteins with Dynamics

PubMed Central

2013-01-01

The genetic missense A30P mutation of the wild-type α-synuclein protein results in the replacement of the 30th amino acid residue from alanine (Ala) to proline (Pro) and was initially found in the members of a German family who developed Parkinson’s disease. Even though the structures of these proteins have been measured before, detailed understanding about the structures and their relationships with free energy landscapes is lacking, which is of interest to provide insights into the pathogenic mechanism of Parkinson’s disease. We report the secondary and tertiary structures and conformational free energy landscapes of the wild-type and A30P mutant-type α-synuclein proteins in an aqueous solution environment via extensive parallel tempering molecular dynamics simulations along with thermodynamic calculations. In addition, we present the residual secondary structure component transition stabilities at the atomic level with dynamics in terms of free energy change calculations using a new strategy that we reported most recently. Our studies yield new interesting results; for instance, we find that the A30P mutation has local as well as long-range effects on the structural properties of the wild-type α-synuclein protein. The helical content at Ala18-Gly31 is less prominent in comparison to the wild-type α-synuclein protein. The β-sheet structure abundance decreases in the N-terminal region upon A30P mutation of the wild-type α-synuclein, whereas the NAC and C-terminal regions possess larger tendencies for β-sheet structure formation. Long-range intramolecular protein interactions are less abundant upon A30P mutation, especially between the NAC and C-terminal regions, which is linked to the less compact and less stable structures of the A30P mutant-type rather than the wild-type α-synuclein protein. Results including the usage of our new strategy for secondary structure transition stabilities show that the A30P mutant-type α-synuclein tendency toward aggregation is higher than the wild-type α-synuclein but we also find that the C-terminal and NAC regions of the A30P mutant-type α-synuclein are reactive toward fibrillzation and aggregation based on atomic level studies with dynamics in an aqueous solution environment. Therefore, we propose that small molecules or drugs blocking the specific residues, which we report herein, located in the NAC- and C-terminal regions of the A30P mutant-type α-synuclein protein might help to reduce the toxicity of the A30P mutant-type α-synuclein protein. PMID:23374072

Structures and free energy landscapes of the wild-type and A30P mutant-type α-synuclein proteins with dynamics.

PubMed

Wise-Scira, Olivia; Aloglu, Ahmet Kemal; Dunn, Aquila; Sakallioglu, Isin Tuna; Coskuner, Orkid

2013-03-20

The genetic missense A30P mutation of the wild-type α-synuclein protein results in the replacement of the 30th amino acid residue from alanine (Ala) to proline (Pro) and was initially found in the members of a German family who developed Parkinson's disease. Even though the structures of these proteins have been measured before, detailed understanding about the structures and their relationships with free energy landscapes is lacking, which is of interest to provide insights into the pathogenic mechanism of Parkinson's disease. We report the secondary and tertiary structures and conformational free energy landscapes of the wild-type and A30P mutant-type α-synuclein proteins in an aqueous solution environment via extensive parallel tempering molecular dynamics simulations along with thermodynamic calculations. In addition, we present the residual secondary structure component transition stabilities at the atomic level with dynamics in terms of free energy change calculations using a new strategy that we reported most recently. Our studies yield new interesting results; for instance, we find that the A30P mutation has local as well as long-range effects on the structural properties of the wild-type α-synuclein protein. The helical content at Ala18-Gly31 is less prominent in comparison to the wild-type α-synuclein protein. The β-sheet structure abundance decreases in the N-terminal region upon A30P mutation of the wild-type α-synuclein, whereas the NAC and C-terminal regions possess larger tendencies for β-sheet structure formation. Long-range intramolecular protein interactions are less abundant upon A30P mutation, especially between the NAC and C-terminal regions, which is linked to the less compact and less stable structures of the A30P mutant-type rather than the wild-type α-synuclein protein. Results including the usage of our new strategy for secondary structure transition stabilities show that the A30P mutant-type α-synuclein tendency toward aggregation is higher than the wild-type α-synuclein but we also find that the C-terminal and NAC regions of the A30P mutant-type α-synuclein are reactive toward fibrillzation and aggregation based on atomic level studies with dynamics in an aqueous solution environment. Therefore, we propose that small molecules or drugs blocking the specific residues, which we report herein, located in the NAC- and C-terminal regions of the A30P mutant-type α-synuclein protein might help to reduce the toxicity of the A30P mutant-type α-synuclein protein.

Anesthetic 2,2,2-trifluoroethanol induces amyloidogenesis and cytotoxicity in human serum albumin.

PubMed

Naeem, Aabgeena; Iram, Afshin; Bhat, Sheraz Ahmed

2015-08-01

Trifluoroethanol (TFE) mimics the membrane environments as it simulates the hydrophobic environment and better stabilizes the secondary structures in peptides owing to its hydrophobicity and hydrogen bond-forming properties. Its dielectric constant approximates that of the interior of proteins and is one-third of that of water. Human serum albumin (HSA) is a biological transporter. The effect of TFE on HSA gives the clue about the conformational changes taking place in HSA on transport of ligands across the biological membranes. At 25% (v/v) and 60% (v/v) TFE, HSA exhibits non-native β-sheet, altered tryptophan fluorescence, exposed hydrophobic clusters, increased thioflavin T fluorescence and prominent red shifted Congo red absorbance, and large hydrodynamic radii suggesting the aggregate formation. Isothermal titration calorimetric results indicate weak binding of TFE and HSA. This suggests that solvent-mediated effects dominate the interaction of TFE and HSA. TEM confirmed prefibrillar at 25% (v/v) and fibrillar aggregates at 60% (v/v) TFE. Comet assay of prefibrillar aggregates showed DNA damage causing cell necrosis hence confirming cytotoxic nature. On increasing concentration of TFE to 80% (v/v), HSA showed retention of native-like secondary structure, increased Trp and ANS fluorescence, a transition from β-sheet to α-helix. Thus, TFE at high concentration possess anti- aggregating potency. Copyright © 2015 Elsevier B.V. All rights reserved.

Teacher Professional Experience and Performance: Impact of the Work Environment and General Welfare in Malaysian Secondary Schools

ERIC Educational Resources Information Center

Malakolunthu, Suseela; Idris, Abdul Rahman; Rengasamy, Nagappan C.

2010-01-01

This study investigated the work environment and general welfare of the Malaysian secondary school teachers. Past studies have explicated that the experience of work environment and general welfare exerted a direct influence on the performance of the teachers, hence student outcome. In the factor analysis, the study identified six factors, namely…

Rural Junior Secondary School Students' Perceptions of Classroom Learning Environments and Their Attitude and Achievement in Mathematics in West China

ERIC Educational Resources Information Center

Yang, Xinrong

2015-01-01

This paper reports findings from a survey of how rural junior secondary school students in the western part of China perceive their mathematics classroom learning environments and associations of learning environment with their attitudes toward mathematics and mathematics achievement. Using adaptations of the widely-used What Is Happening In this…

Cultural learning environment of upper secondary science students

NASA Astrophysics Data System (ADS)

Dhindsa, Harkirat S.

2005-05-01

The aims of this research were to validate the Cultural Learning Environment Questionnaire in the Brunei context and to evaluate culturally sensitive factors (gender equity, collaboration, deference, competition, teacher authority, modelling and congruence) of upper secondary students’ learning environment. The subjects of this study were 831 upper secondary science students from coeducational schools in Brunei. The data were collected by administering the Cultural Learning Environment Instrument developed by Fisher and Waldrip. Factor analysis and reliability results showed that the instrument was suitable for evaluating the six culturally sensitive factors associated with the cultural learning environment of Bruneian upper secondary students. The results also suggested that students believed both genders were treated equally in their classes. The students viewed that they were to some extent dependent learners; however, they were willing to give their independent views in their classes. The data also suggest that students perceived that they were equally cooperative and competitive. The culturally sensitive factors of the students’ cultural learning environment were not influenced by their gender, but regional variations in values for some of these factors were observed. Further research has been recommended to investigate how the students were equally cooperative and competitive, as well as what factors contributed to the regional differences.

Do family and neighbourhood matter in secondary school completion? A multilevel study of determinants and their interactions in a life-course perspective

PubMed Central

Myhr, Arnhild; Lillefjell, Monica; Espnes, Geir Arild; Halvorsen, Thomas

2017-01-01

Background Completion of secondary education is important for individuals’ future health and health behaviour. The fundamental purpose of this study is to investigate the variation and clustering of school completion in families and neighbourhoods. Secondly, we aim to examine the impact of individuals’ family structure and neighbourhood of residence and examine to what extent parental education level moderates these associations. Methods Longitudinal register data for 30% of the entire Norwegian population aged 21–27 years in 2010 (N = 107,003) was extracted from Statistic Norway´s event database. Three-level logistic regression models, which incorporated individual, family, and neighbourhood contextual factors, were applied to estimate the family and neighbourhood general contextual effects and detect possible educational differences in the impact of family structure and urban place of residence in school completion. Results Completion rates were significantly higher within families with higher education level (79% in tertiary educated families vs. 61% and 48% in secondary and primary educated families respectively) and were strongly correlated within families (ICC = 39.6) and neighbourhoods (ICC = 5.7). Several structural factors at the family level negatively associated with school completion (e.g., family disruption, large family size, and young maternal age) were more prevalent and displayed more negative impact among primary educated individuals. Urban residence was associated with school completion, but only among the tertiary educated. Conclusions Investment in the resources in the individuals’ immediate surroundings, including family and neighbourhood, may address a substantial portion of the social inequalities in the completion of upper secondary education. The high intra-familial correlation in school completion suggests that public health policies and future research should acknowledge family environments in order to improve secondary education completion rates among young people within lower educated families. PMID:28222115

RNA Secondary Structure Prediction by Using Discrete Mathematics: An Interdisciplinary Research Experience for Undergraduate Students

ERIC Educational Resources Information Center

Ellington, Roni; Wachira, James; Nkwanta, Asamoah

2010-01-01

The focus of this Research Experience for Undergraduates (REU) project was on RNA secondary structure prediction by using a lattice walk approach. The lattice walk approach is a combinatorial and computational biology method used to enumerate possible secondary structures and predict RNA secondary structure from RNA sequences. The method uses…

Fourier-based classification of protein secondary structures.

PubMed

Shu, Jian-Jun; Yong, Kian Yan

2017-04-15

The correct prediction of protein secondary structures is one of the key issues in predicting the correct protein folded shape, which is used for determining gene function. Existing methods make use of amino acids properties as indices to classify protein secondary structures, but are faced with a significant number of misclassifications. The paper presents a technique for the classification of protein secondary structures based on protein "signal-plotting" and the use of the Fourier technique for digital signal processing. New indices are proposed to classify protein secondary structures by analyzing hydrophobicity profiles. The approach is simple and straightforward. Results show that the more types of protein secondary structures can be classified by means of these newly-proposed indices. Copyright © 2017 Elsevier Inc. All rights reserved.

Structures and Free Energy Landscapes of the A53T Mutant-Type α-Synuclein Protein and Impact of A53T Mutation on the Structures of the Wild-Type α-Synuclein Protein with Dynamics

PubMed Central

2013-01-01

The A53T genetic missense mutation of the wild-type α-synuclein (αS) protein was initially identified in Greek and Italian families with familial Parkinson’s disease. Detailed understanding of the structures and the changes induced in the wild-type αS structure by the A53T mutation, as well as establishing the direct relationships between the rapid conformational changes and free energy landscapes of these intrinsically disordered fibrillogenic proteins, helps to enhance our fundamental knowledge and to gain insights into the pathogenic mechanism of Parkinson’s disease. We employed extensive parallel tempering molecular dynamics simulations along with thermodynamic calculations to determine the secondary and tertiary structural properties as well as the conformational free energy surfaces of the wild-type and A53T mutant-type αS proteins in an aqueous solution medium using both implicit and explicit water models. The confined aqueous volume effect in the simulations of disordered proteins using an explicit model for water is addressed for a model disordered protein. We also assessed the stabilities of the residual secondary structure component interconversions in αS based on free energy calculations at the atomic level with dynamics using our recently developed theoretical strategy. To the best of our knowledge, this study presents the first detailed comparison of the structural properties linked directly to the conformational free energy landscapes of the monomeric wild-type and A53T mutant-type α-synuclein proteins in an aqueous solution environment. Results demonstrate that the β-sheet structure is significantly more altered than the helical structure upon A53T mutation of the monomeric wild-type αS protein in aqueous solution. The β-sheet content close to the mutation site in the N-terminal region is more abundant while the non-amyloid-β component (NAC) and C-terminal regions show a decrease in β-sheet abundance upon A53T mutation. Obtained results utilizing our new theoretical strategy show that the residual secondary structure conversion stabilities resulting in α-helix formation are not significantly affected by the mutation. Interestingly, the residual secondary structure conversion stabilities show that secondary structure conversions resulting in β-sheet formation are influenced by the A53T mutation and the most stable residual transition yielding β-sheet occurs directly from the coil structure. Long-range interactions detected between the NAC region and the N- or C-terminal regions of the wild-type αS disappear upon A53T mutation. The A53T mutant-type αS structures are thermodynamically more stable than those of the wild-type αS protein structures in aqueous solution. Overall, the higher propensity of the A53T mutant-type αS protein to aggregate in comparison to the wild-type αS protein is related to the increased β-sheet formation and lack of strong intramolecular long-range interactions in the N-terminal region in comparison to its wild-type form. The specific residual secondary structure component stabilities reported herein provide information helpful for designing and synthesizing small organic molecules that can block the β-sheet forming residues, which are reactive toward aggregation. PMID:23607785

Structures and free energy landscapes of the A53T mutant-type α-synuclein protein and impact of A53T mutation on the structures of the wild-type α-synuclein protein with dynamics.

PubMed

Coskuner, Orkid; Wise-Scira, Olivia

2013-07-17

The A53T genetic missense mutation of the wild-type α-synuclein (αS) protein was initially identified in Greek and Italian families with familial Parkinson's disease. Detailed understanding of the structures and the changes induced in the wild-type αS structure by the A53T mutation, as well as establishing the direct relationships between the rapid conformational changes and free energy landscapes of these intrinsically disordered fibrillogenic proteins, helps to enhance our fundamental knowledge and to gain insights into the pathogenic mechanism of Parkinson's disease. We employed extensive parallel tempering molecular dynamics simulations along with thermodynamic calculations to determine the secondary and tertiary structural properties as well as the conformational free energy surfaces of the wild-type and A53T mutant-type αS proteins in an aqueous solution medium using both implicit and explicit water models. The confined aqueous volume effect in the simulations of disordered proteins using an explicit model for water is addressed for a model disordered protein. We also assessed the stabilities of the residual secondary structure component interconversions in αS based on free energy calculations at the atomic level with dynamics using our recently developed theoretical strategy. To the best of our knowledge, this study presents the first detailed comparison of the structural properties linked directly to the conformational free energy landscapes of the monomeric wild-type and A53T mutant-type α-synuclein proteins in an aqueous solution environment. Results demonstrate that the β-sheet structure is significantly more altered than the helical structure upon A53T mutation of the monomeric wild-type αS protein in aqueous solution. The β-sheet content close to the mutation site in the N-terminal region is more abundant while the non-amyloid-β component (NAC) and C-terminal regions show a decrease in β-sheet abundance upon A53T mutation. Obtained results utilizing our new theoretical strategy show that the residual secondary structure conversion stabilities resulting in α-helix formation are not significantly affected by the mutation. Interestingly, the residual secondary structure conversion stabilities show that secondary structure conversions resulting in β-sheet formation are influenced by the A53T mutation and the most stable residual transition yielding β-sheet occurs directly from the coil structure. Long-range interactions detected between the NAC region and the N- or C-terminal regions of the wild-type αS disappear upon A53T mutation. The A53T mutant-type αS structures are thermodynamically more stable than those of the wild-type αS protein structures in aqueous solution. Overall, the higher propensity of the A53T mutant-type αS protein to aggregate in comparison to the wild-type αS protein is related to the increased β-sheet formation and lack of strong intramolecular long-range interactions in the N-terminal region in comparison to its wild-type form. The specific residual secondary structure component stabilities reported herein provide information helpful for designing and synthesizing small organic molecules that can block the β-sheet forming residues, which are reactive toward aggregation.

X-ray photoelectron spectroscopy and secondary electron yield analysis of Al and Cu samples exposed to an accelerator environment

NASA Astrophysics Data System (ADS)

Rosenberg, R. A.; McDowell, M. W.; Ma, Q.; Harkay, K. C.

2003-09-01

It is well known that exposure to an accelerator environment can cause ``conditioning'' of the vacuum chamber surfaces. In order to understand the manner in which the surface structure might influence the production of gases and electrons in the accelerator, such surfaces should be studied both before and after exposure to accelerator conditions. Numerous studies have been performed on representative materials prior to being inserted into an accelerator, but very little has been done on materials that have ``lived'' in the accelerator for extended periods. In the present work, we mounted Al and Cu coupons at different positions in a section of the Advanced Photon Source storage ring and removed them following exposures ranging from 6 to 18 months. X-ray photoelectron spectroscopy (XPS) of the surface was performed before and after exposure. Changes were observed that depended on the location and whether the coupon was facing the chamber interior or chamber wall. These results will be presented and compared to XPS and secondary electron yield data obtained from laboratory measurements meant to simulate the accelerator conditions.

Bismaleimides and related maleimido polymers as matrix resins

NASA Technical Reports Server (NTRS)

Parker, J. A.; Kourtides, D. A.; Fohlen, G. M.

1985-01-01

Significant processing and property improvements can be achieved by copolymerization of state-of-the-art bisimides with various vinyl stilbazole derivatives to give both fire resistance and high-temperature properties from hot-melt compositions. Significant improvement in mechanical properties is achieved through these modifications, which may make these new matrix resins ideal candidates for fireworthy secondary graphite composite structures. Phosphorous modifications of maleimido polymers through phosphonate structure and tricyclophosphazene derivatives provide families of new matrix resins for short-time applications in severe thermo-oxidative environments. With further research these may provide matrix resins for long-term thermo-oxidative stability of advanced composites at temperatures up to 400 to 500 C.

Deciphering the shape and deformation of secondary structures through local conformation analysis

PubMed Central

2011-01-01

Background Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Results Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface) reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. Conclusion The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons. PMID:21284872

Deciphering the shape and deformation of secondary structures through local conformation analysis.

PubMed

Baussand, Julie; Camproux, Anne-Claude

2011-02-01

Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface) reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons.

SFG analysis of surface bound proteins: a route towards structure determination.

PubMed

Weidner, Tobias; Castner, David G

2013-08-14

The surface of a material is rapidly covered with proteins once that material is placed in a biological environment. The structure and function of these bound proteins play a key role in the interactions and communications of the material with the biological environment. Thus, it is crucial to gain a molecular level understanding of surface bound protein structure. While X-ray diffraction and solution phase NMR methods are well established for determining the structure of proteins in the crystalline or solution phase, there is not a corresponding single technique that can provide the same level of structural detail about proteins at surfaces or interfaces. However, recent advances in sum frequency generation (SFG) vibrational spectroscopy have significantly increased our ability to obtain structural information about surface bound proteins and peptides. A multi-technique approach of combining SFG with (1) protein engineering methods to selectively introduce mutations and isotopic labels, (2) other experimental methods such as time-of-flight secondary ion mass spectrometry (ToF-SIMS) and near edge X-ray absorption fine structure (NEXAFS) to provide complementary information, and (3) molecular dynamic (MD) simulations to extend the molecular level experimental results is a particularly promising route for structural characterization of surface bound proteins and peptides. By using model peptides and small proteins with well-defined structures, methods have been developed to determine the orientation of both backbone and side chains to the surface.

SFG analysis of surface bound proteins: A route towards structure determination

PubMed Central

Weidner, Tobias; Castner, David G.

2013-01-01

The surface of a material is rapidly covered with proteins once that material is placed in a biological environment. The structure and function of these bound proteins play a key role in the interactions and communications of the material with the biological environment. Thus, it is crucial to gain a molecular level understanding of surface bound protein structure. While X-ray diffraction and solution phase NMR methods are well established for determining the structure of proteins in the crystalline or solution phase, there is not a corresponding single technique that can provide the same level of structural detail about proteins at surfaces or interfaces. However, recent advances in sum frequency generation (SFG) vibrational spectroscopy have significantly increased our ability to obtain structural information about surface bound proteins and peptides. A multi-technique approach of combining SFG with (1) protein engineering methods to selectively introduce mutations and isotopic labels, (2) other experimental methods such as time-of-flight secondary ion mass spectrometry (ToF-SIMS) and near edge x-ray absorption fine structure (NEXAFS) to provide complementary information, and (3) molecular dynamic (MD) simulations to extend the molecular level experimental results is a particularly promising route for structural characterization of surface bound proteins and peptides. By using model peptides and small proteins with well-defined structures, methods have been developed to determine the orientation of both backbone and side chains to the surface. PMID:23727992

Student control ideology and the science classroom environment in urban secondary schools of sudan

NASA Astrophysics Data System (ADS)

Harty, Harold; Hassan, Hassan A.

An examination was made concerning the relationships between Sudanese secondary science teachers' pupil control ideology and their students' perceptions/observations of the psychosocial environment of their science classrooms. One hundred secondary science teachers were classified as possessing humanistic (N = 20) or custodial (N = 20) control ideologies. A class (N = 40) of students was randomly selected for every teacher in both groups. The findings revealed that no significant relationships existed between the control ideologies of the teachers and their students' perceptions/observations of the classroom environment. Custodialism in control ideology was significantly related to the classroom environment psychosocial aspect of low support. Discussion and implications of the findings have been approached from both Sudanese and American perspectives.

40 CFR 50.2 - Scope.

Code of Federal Regulations, 2012 CFR

2012-07-01

... of safety, to protect the public health. National secondary ambient air quality standards define... 40 Protection of Environment 2 2012-07-01 2012-07-01 false Scope. 50.2 Section 50.2 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS NATIONAL PRIMARY AND SECONDARY AMBIENT...

Predicting the performance of a strategic alliance: an analysis of the Community Clinical Oncology Program.

PubMed

Kaluzny, A D; Lacey, L M; Warnecke, R; Hynes, D M; Morrissey, J; Ford, L; Sondik, E

1993-06-01

This study is designed to examine the effects of environment and structure of the Community Clinical Oncology Program (CCOP) on performance as measured by patient accrual to National Cancer Institute (NCI)-approved treatment protocols. Data and analysis are part of a larger evaluation of the NCI Community Clinical Oncology Program during its second funding cycle, June 1987-May 1990. Data, taken from primary and secondary sources, included a survey of selected informants in CCOPs and research bases, CCOP grant applications, CCOP annual progress reports, and site visits to a subsample of CCOPs (N = 20) and research bases (N = 5). Accrual data were obtained from NCI records. Analysis involved three complementary sets of factors: the local health care resources environment available to the CCOP, the larger policy environment as reflected by the relationship of the CCOP to selected research bases and the NCI, and the operational structure of the CCOP itself. A hierarchical model examined the separate and cumulative effects of local and policy environment and structure on performance. Other things equal, the primary predictors of treatment accrual were: (1) the larger policy environment, as measured by the attendance of nurses at research base meetings; and (2) operational structure, as measured by the number and character of components within participating CCOPs and the number of hours per week worked by data managers. These factors explained 73 percent of the total variance in accrual performance. Findings suggest criteria for selecting the types of organizations to participate in the alliance, as well as for establishing guidelines for managing such alliances. A future challenge is to determine the extent to which factors predicting accrual to cancer treatment clinical trials are equally important as predictors of accrual to cancer prevention and control trials.

Protein folding, misfolding and aggregation: The importance of two-electron stabilizing interactions

PubMed Central

2017-01-01

Proteins associated with neurodegenerative diseases are highly pleiomorphic and may adopt an all-α-helical fold in one environment, assemble into all-β-sheet or collapse into a coil in another, and rapidly polymerize in yet another one via divergent aggregation pathways that yield broad diversity of aggregates’ morphology. A thorough understanding of this behaviour may be necessary to develop a treatment for Alzheimer’s and related disorders. Unfortunately, our present comprehension of folding and misfolding is limited for want of a physicochemical theory of protein secondary and tertiary structure. Here we demonstrate that electronic configuration and hyperconjugation of the peptide amide bonds ought to be taken into account to advance such a theory. To capture the effect of polarization of peptide linkages on conformational and H-bonding propensity of the polypeptide backbone, we introduce a function of shielding tensors of the Cα atoms. Carrying no information about side chain-side chain interactions, this function nonetheless identifies basic features of the secondary and tertiary structure, establishes sequence correlates of the metamorphic and pH-driven equilibria, relates binding affinities and folding rate constants to secondary structure preferences, and manifests common patterns of backbone density distribution in amyloidogenic regions of Alzheimer’s amyloid β and tau, Parkinson’s α-synuclein and prions. Based on those findings, a split-intein like mechanism of molecular recognition is proposed to underlie dimerization of Aβ, tau, αS and PrPC, and divergent pathways for subsequent association of dimers are outlined; a related mechanism is proposed to underlie formation of PrPSc fibrils. The model does account for: (i) structural features of paranuclei, off-pathway oligomers, non-fibrillar aggregates and fibrils; (ii) effects of incubation conditions, point mutations, isoform lengths, small-molecule assembly modulators and chirality of solid-liquid interface on the rate and morphology of aggregation; (iii) fibril-surface catalysis of secondary nucleation; and (iv) self-propagation of infectious strains of mammalian prions. PMID:28922400

Influence of Aqueous-Salt Conditions on the Structure and Dynamics of the Monomeric and Novel Dimeric forms of the Alzheimer s ABeta21-30 protein fragment

NASA Astrophysics Data System (ADS)

Smith, Micholas Dean

The behavior of the Alzheimer's related peptide Abeta is the subject of much study. In typical computational studies the environment local to the peptide is assumed to be pure water; however, in vivo the peptide is found in the extracellular space near the plasma membrane which is rich in ionic species. In this thesis, the hypothesis that the presence of group I/IIA salts will result in increased sampling of disordered structures as well as modify the dynamics of meta-stable structural motifs in the small folding nucleus of the Abeta peptide (Abeta21-30) is examined under a variety of ionic environments and was shown that of the tested salts, CaCl2 (and MgCl2, to a much lesser degree) did increase the propensity for disordered states; while, the group IA salts, KCl and NaCl, had little effect on the secondary structure of the peptide. Further, study of three familial mutations of this peptide region is also performed under aqueous salt-environments to elucidate further mechanistic details of how aqueous salts modify the region's behavior. Finally, as experimental results have highlighted that aggregation rates of the full-length peptide are modified by the presence of CaCl2, this work examines novel dimers states of Abeta21-30 and their stabilities when exposed to CaCl2.

Influence of thermodynamically unfavorable secondary structures on DNA hybridization kinetics

PubMed Central

Hata, Hiroaki; Kitajima, Tetsuro

2018-01-01

Abstract Nucleic acid secondary structure plays an important role in nucleic acid–nucleic acid recognition/hybridization processes, and is also a vital consideration in DNA nanotechnology. Although the influence of stable secondary structures on hybridization kinetics has been characterized, unstable secondary structures, which show positive ΔG° with self-folding, can also form, and their effects have not been systematically investigated. Such thermodynamically unfavorable secondary structures should not be ignored in DNA hybridization kinetics, especially under isothermal conditions. Here, we report that positive ΔG° secondary structures can change the hybridization rate by two-orders of magnitude, despite the fact that their hybridization obeyed second-order reaction kinetics. The temperature dependence of hybridization rates showed non-Arrhenius behavior; thus, their hybridization is considered to be nucleation limited. We derived a model describing how ΔG° positive secondary structures affect hybridization kinetics in stopped-flow experiments with 47 pairs of oligonucleotides. The calculated hybridization rates, which were based on the model, quantitatively agreed with the experimental rate constant. PMID:29220504

What Learning Environments Best Address 21st-Century Students' Perceived Needs at the Secondary Level of Instruction?

ERIC Educational Resources Information Center

Lemley, J. Brett; Schumacher, Gary; Vesey, Winona

2014-01-01

The purpose of a recent study was to determine what learning environments best address the needs of 21st-century students at the secondary level. This study concluded that the presence of a positive 21st-century learning environment is related to student satisfaction and student-teacher relationships. While the majority of the literature on…

Influence of Learning Environment on Students' Academic Achievement in Mathematics: A Case Study of Some Selected Secondary Schools in Yobe State-Nigeria

ERIC Educational Resources Information Center

Shamaki, Timothy Ado

2015-01-01

The purpose of the study was to determine the influence of learning environment on students' academic achievement in mathematics at senior secondary school level. Thus the study investigated some components of learning environment and their possible influence on students' academic achievement in mathematics. A sample of 337 randomly selected SS II…

The Inclusion of Chitosan in Poly-ε-caprolactone Nanoparticles: Impact on the Delivery System Characteristics and on the Adsorbed Ovalbumin Secondary Structure.

PubMed

Jesus, Sandra; Fragal, Elizangela H; Rubira, Adley F; Muniz, Edvani C; Valente, Artur J M; Borges, Olga

2018-01-01

This report extensively explores the benefits of including chitosan into poly-ε-caprolactone (PCL) nanoparticles (NPs) to obtain an improved protein/antigen delivery system. Blend NPs (PCL/chitosan NPs) showed improved protein adsorption efficacy (84%) in low shear stress and aqueous environment, suggesting that a synergistic effect between PCL hydrophobic nature and the positive charges of chitosan present at the particle surface was responsible for protein interaction. Additionally, thermal analysis suggested the blend NPs were more stable than the isolated polymers and cytotoxicity assays in a primary cell culture revealed chitosan inclusion in PCL NPs reduced the toxicity of the delivery system. A quantitative 6-month stability study showed that the inclusion of chitosan in PCL NPs did not induce a change in adsorbed ovalbumin (OVA) secondary structure characterized by the increase in the unordered conformation (random coil), as it was observed for OVA adsorbed to chitosan NPs. Additionally, the slight conformational changes occurred, are not expected to compromise ovalbumin secondary structure and activity, during a 6-month storage even at high temperatures (45°C). In simulated biological fluids, PCL/chitosan NPs showed an advantageous release profile for oral delivery. Overall, the combination of PCL and chitosan characteristics provide PCL/chitosan NPs valuable features particularly important to the development of vaccines for developing countries, where it is difficult to ensure cold chain transportation and non-parenteral formulations would be preferred.

Marine Science Syllabus for Secondary Schools. Report of an IOC Workshop on the Preparation of a Marine Science Syllabus for Secondary Schools. Unesco Reports in Marine Science, 5.

ERIC Educational Resources Information Center

United Nations Educational, Scientific, and Cultural Organization, Paris (France). Div. of Marine Sciences.

Presented is a syllabus for introducing oceanography and the marine environment into the secondary school curricula of all IOC Member States, whether developed or developing. The main purpose of the syllabus is to promote an understanding of oceanography and the marine environment. The syllabus is action- and output-oriented, as well as…

Examining the Behavior and Thinking Levels of Secondary School Students (6th-8th Grades) towards the Environment According to Gender

ERIC Educational Resources Information Center

Durkan, Nazmi

2017-01-01

The aim of this study is to examine the behavior and thinking levels of secondary school students towards the environment according to grade and gender. Relational screening model was used for the study. The sample includes a total of 958 (512 females and 446 males) secondary school students. Of the participants, 261 (27.2%) are in 6th grade, 461…

The Positive Environmental Contribution of Jarosite by Retaining Lead in Acid Mine Drainage Areas

PubMed Central

Figueiredo, Maria-Ondina; da Silva, Teresa Pereira

2011-01-01

Jarosite, KFe3(SO4)2(OH)6, is a secondary iron sulphate often found in acid mine drainage (AMD) environments, particularly in mining wastes from polymetallic sulphide ore deposits. Despite the negative environmental connotation usually ascribed to secondary sulphate minerals due to the release of hazardous elements to aquifers and soils, jarosite acts as an efficient remover and immobilizer of such metals, particularly lead. The mineral chemistry of jarosite is reviewed and the results of a Fe K-edge XANES (X-Ray Absorption Near-Edge Structure) study of K-, Na- and Pb-jarosite are described and discussed within the context of the abandoned old mines of São Domingos and Aljustrel located in southern Portugal, in the Iberian Pyrite Belt (IPB). PMID:21655138

On the chemistry, toxicology and genetics of the cyanobacterial toxins, microcystin, nodularin, saxitoxin and cylindrospermopsin.

PubMed

Pearson, Leanne; Mihali, Troco; Moffitt, Michelle; Kellmann, Ralf; Neilan, Brett

2010-05-10

The cyanobacteria or "blue-green algae", as they are commonly termed, comprise a diverse group of oxygenic photosynthetic bacteria that inhabit a wide range of aquatic and terrestrial environments, and display incredible morphological diversity. Many aquatic, bloom-forming species of cyanobacteria are capable of producing biologically active secondary metabolites, which are highly toxic to humans and other animals. From a toxicological viewpoint, the cyanotoxins span four major classes: the neurotoxins, hepatotoxins, cytotoxins, and dermatoxins (irritant toxins). However, structurally they are quite diverse. Over the past decade, the biosynthesis pathways of the four major cyanotoxins: microcystin, nodularin, saxitoxin and cylindrospermopsin, have been genetically and biochemically elucidated. This review provides an overview of these biosynthesis pathways and additionally summarizes the chemistry and toxicology of these remarkable secondary metabolites.

Assessing the validity of commercial and municipal food environment data sets in Vancouver, Canada.

PubMed

Daepp, Madeleine Ig; Black, Jennifer

2017-10-01

The present study assessed systematic bias and the effects of data set error on the validity of food environment measures in two municipal and two commercial secondary data sets. Sensitivity, positive predictive value (PPV) and concordance were calculated by comparing two municipal and two commercial secondary data sets with ground-truthed data collected within 800 m buffers surrounding twenty-six schools. Logistic regression examined associations of sensitivity and PPV with commercial density and neighbourhood socio-economic deprivation. Kendall's τ estimated correlations between density and proximity of food outlets near schools constructed with secondary data sets v. ground-truthed data. Vancouver, Canada. Food retailers located within 800 m of twenty-six schools RESULTS: All data sets scored relatively poorly across validity measures, although, overall, municipal data sets had higher levels of validity than did commercial data sets. Food outlets were more likely to be missing from municipal health inspections lists and commercial data sets in neighbourhoods with higher commercial density. Still, both proximity and density measures constructed from all secondary data sets were highly correlated (Kendall's τ>0·70) with measures constructed from ground-truthed data. Despite relatively low levels of validity in all secondary data sets examined, food environment measures constructed from secondary data sets remained highly correlated with ground-truthed data. Findings suggest that secondary data sets can be used to measure the food environment, although estimates should be treated with caution in areas with high commercial density.

Diversity of exophillic acid derivatives in strains of an endophytic Exophiala sp.

PubMed

Cheikh-Ali, Zakaria; Glynou, Kyriaki; Ali, Tahir; Ploch, Sebastian; Kaiser, Marcel; Thines, Marco; Bode, Helge B; Maciá-Vicente, Jose G

2015-10-01

Members of the fungal genus Exophiala are common saprobes in soil and water environments, opportunistic pathogens of animals, or endophytes in plant roots. Their ecological versatility could imply a capacity to produce diverse secondary metabolites, but only a few studies have aimed at characterizing their chemical profiles. Here, we assessed the secondary metabolites produced by five Exophiala sp. strains of a particular phylotype, isolated from roots of Microthlaspi perfoliatum growing in different European localities. Exophillic acid and two previously undescribed compounds were isolated from these strains, and their structures were elucidated by spectroscopic methods using MS, 1D and 2D NMR. Bioassays revealed a weak activity of these compounds against disease-causing protozoa and mammalian cells. In addition, 18 related structures were identified by UPLC/MS based on comparisons with the isolated structures. Three Exophiala strains produced derivatives containing a β-d-glucopyranoside moiety, and their colony morphology was distinct from the other two strains, which produced derivatives lacking β-d-glucopyranoside. Whether the chemical/morphological strain types represent variants of the same genotype or independent genetic populations within Exophiala remains to be evaluated. Copyright © 2015 Elsevier Ltd. All rights reserved.

40 CFR 143.3 - Secondary maximum contaminant levels.

Code of Federal Regulations, 2013 CFR

2013-07-01

.... 143.3 Section 143.3 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL SECONDARY DRINKING WATER REGULATIONS § 143.3 Secondary maximum contaminant levels. The secondary maximum contaminant levels for public water systems are as follows: Contaminant...

40 CFR 143.3 - Secondary maximum contaminant levels.

Code of Federal Regulations, 2011 CFR

2011-07-01

.... 143.3 Section 143.3 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL SECONDARY DRINKING WATER REGULATIONS § 143.3 Secondary maximum contaminant levels. The secondary maximum contaminant levels for public water systems are as follows: Contaminant...

40 CFR 143.3 - Secondary maximum contaminant levels.

Code of Federal Regulations, 2014 CFR

2014-07-01

.... 143.3 Section 143.3 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL SECONDARY DRINKING WATER REGULATIONS § 143.3 Secondary maximum contaminant levels. The secondary maximum contaminant levels for public water systems are as follows: Contaminant...

40 CFR 143.3 - Secondary maximum contaminant levels.

Code of Federal Regulations, 2012 CFR

2012-07-01

.... 143.3 Section 143.3 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL SECONDARY DRINKING WATER REGULATIONS § 143.3 Secondary maximum contaminant levels. The secondary maximum contaminant levels for public water systems are as follows: Contaminant...

An Assessment of Science Teachers' Perceptions of Secondary School Environments in Taiwan

NASA Astrophysics Data System (ADS)

Huang, Shwu-Yong L.

2006-01-01

This study investigates the psychosocial environments of secondary schools from science teachers’ perspectives, as well as associated variables. Using a sample of 900 secondary science teachers from 52 schools in Taiwan, the results attest to the validity and reliability of the instrument, the Science Teacher School Environment Questionnaire, and its ability to differentiate among schools. The descriptive results show that a majority of science teachers positively perceived their school environments. The teachers reported high collegiality, good teacher student relations, effective principal leadership, strong professional interest, and low work pressure—but also low staff freedom. Multiple regression results further indicate that policy-relevant variables like school level, school location, and teachers’ intentions to stay in teaching were associated with science teachers’ perceptions of their school environments. Qualitative data analysis based on interviews of 34 science teachers confirmed and enriched these findings.

Marine Microbial Secondary Metabolites: Pathways, Evolution and Physiological Roles.

PubMed

Giordano, Daniela; Coppola, Daniela; Russo, Roberta; Denaro, Renata; Giuliano, Laura; Lauro, Federico M; di Prisco, Guido; Verde, Cinzia

2015-01-01

Microbes produce a huge array of secondary metabolites endowed with important ecological functions. These molecules, which can be catalogued as natural products, have long been exploited in medical fields as antibiotics, anticancer and anti-infective agents. Recent years have seen considerable advances in elucidating natural-product biosynthesis and many drugs used today are natural products or natural-product derivatives. The major contribution to recent knowledge came from application of genomics to secondary metabolism and was facilitated by all relevant genes being organised in a contiguous DNA segment known as gene cluster. Clustering of genes regulating biosynthesis in bacteria is virtually universal. Modular gene clusters can be mixed and matched during evolution to generate structural diversity in natural products. Biosynthesis of many natural products requires the participation of complex molecular machines known as polyketide synthases and non-ribosomal peptide synthetases. Discovery of new evolutionary links between the polyketide synthase and fatty acid synthase pathways may help to understand the selective advantages that led to evolution of secondary-metabolite biosynthesis within bacteria. Secondary metabolites confer selective advantages, either as antibiotics or by providing a chemical language that allows communication among species, with other organisms and their environment. Herewith, we discuss these aspects focusing on the most clinically relevant bioactive molecules, the thiotemplated modular systems that include polyketide synthases, non-ribosomal peptide synthetases and fatty acid synthases. We begin by describing the evolutionary and physiological role of marine natural products, their structural/functional features, mechanisms of action and biosynthesis, then turn to genomic and metagenomic approaches, highlighting how the growing body of information on microbial natural products can be used to address fundamental problems in environmental evolution and biotechnology. © 2015 Elsevier Ltd. All rights reserved.

Uncovering Mechanisms for Repair and Protection in Cold Environments Through Studies of Cold Adapted Archaea

DTIC Science & Technology

2009-12-18

Cpn60) subunits is more abundant during growth at 4°C compared to 23°C. Consistent with this, cold shock studies in thermophilic archaea, and...helicases (Mbur_0245, Mbur_1950): These enzymes may be responsible for unwinding secondary structures in messenger RNA, and a role in cold adaptation in M...limiting step, it is unsurprising that these enzymes showed higher abundance at 4ºC. ParA protein (Mbur_2141): ParA ATPases are a ubiquitous

The dynamics of interacting salt structures and associated fluid flow in the western Norwegian-Danish Basin

NASA Astrophysics Data System (ADS)

Olsen, Mikkel S.; Clausen, Ole R.; Andresen, Katrine J.; Korstgård, John A.

2015-04-01

Minor secondary structures observed along the flanks of major salt structures in the Norwegian-Danish Basin appear to be generated mainly during the early stages of halokinesis. Seismic anomalies in the cover sediments at the flanks of the major salt structures and in relation to one of the secondary structures show several circular patterns. The circular patterns are generally interpreted as faults related to collapsing salt, indicating a subtle and dynamic cannibalization relationship between the secondary structure and the main diapir. High-amplitude reflections interpreted as either entrapped gas along the circular faults or diagenetic changes induced by the fluids originating from the salt-sediment interface generally enhances the seismic appearance of the circular faults, but potentially also disturb the seismic imaging of the faults. Other secondary salt structures, with a similar geometry, do not show sign of collapse, apparently due to a greater distance from the main salt structures and therefore not within the reach of being cannibalized by these. The observations furthermore suggest a trend showing a more advanced development of the main salt structures when the secondary structures are cannibalized. The lateral distribution of the main salt structures thus appears to be controlled not only by the initial thickness of the Zechstein salt, and possible underlying structures, but also by subtle variations in the location and evolution of secondary structures. The secondary structures have a major impact on the drainage of the deep Mesozoic succession as indicated by the fluid flow pattern also observed in the study, which emphasizes that a detailed mapping of salt structures including secondary structures at the flanks is of major importance during evaluation of petroleum systems in areas dominated by halokinesis.

The Role Of Environment In Stellar Mass Growth

NASA Astrophysics Data System (ADS)

Thomas, Daniel

2017-06-01

In this talk I give a brief summary of methods to measure galaxy environment. I then discuss the dependence of stellar population properties on environmental density: it turns out that the latter are driven by galaxy mass, and galaxy environment only plays a secondary role, mostly at late times in low-mass galaxies. I show that this evidence has now been extended to stellar population gradients using the IFU survey SDSS/MaNGA that again turn out to be independent of environment, including central-satellite classification. Finally I present results from the DES, where the dependence of the stellar mass function with redshift and environmental density is explored. It is found that the fraction of massive galaxies is larger in high density environments than in low density environments. The low density and high density components converge with increasing redshift up to z 1.0 where the shapes of the mass function components are indistinguishable. This study shows how high density structures build up around massive galaxies through cosmic time, which sets new valuable constraints on galaxy formation models.

40 CFR 421.260 - Applicability: Description of the secondary precious metals subcategory.

Code of Federal Regulations, 2010 CFR

2010-07-01

... secondary precious metals subcategory. 421.260 Section 421.260 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS NONFERROUS METALS MANUFACTURING POINT SOURCE CATEGORY Secondary Precious Metals Subcategory § 421.260 Applicability: Description of the secondary...

Membrane transporters studied by EPR spectroscopy: structure determination and elucidation of functional dynamics.

PubMed

Mullen, Anna; Hall, Jenny; Diegel, Janika; Hassan, Isa; Fey, Adam; MacMillan, Fraser

2016-06-15

During their mechanistic cycles membrane transporters often undergo extensive conformational changes, sampling a range of orientations, in order to complete their function. Such membrane transporters present somewhat of a challenge to conventional structural studies; indeed, crystallization of membrane-associated proteins sometimes require conditions that vary vastly from their native environments. Moreover, this technique currently only allows for visualization of single selected conformations during any one experiment. EPR spectroscopy is a magnetic resonance technique that offers a unique opportunity to study structural, environmental and dynamic properties of such proteins in their native membrane environments, as well as readily sampling their substrate-binding-induced dynamic conformational changes especially through complementary computational analyses. Here we present a review of recent studies that utilize a variety of EPR techniques in order to investigate both the structure and dynamics of a range of membrane transporters and associated proteins, focusing on both primary (ABC-type transporters) and secondary active transporters which were key interest areas of the late Professor Stephen Baldwin to whom this review is dedicated. © 2016 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

40 CFR 50.12 - National primary and secondary ambient air quality standards for lead.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 2 2010-07-01 2010-07-01 false National primary and secondary ambient... AGENCY (CONTINUED) AIR PROGRAMS NATIONAL PRIMARY AND SECONDARY AMBIENT AIR QUALITY STANDARDS § 50.12 National primary and secondary ambient air quality standards for lead. (a) National primary and secondary...

Secondary GIS built environment data for health research: guidance for data development

PubMed Central

Stewart, Orion T.; Carlos, Heather A.; Lee, Chanam; Berke, Ethan M.; Hurvitz, Philip M.; Li, Li; Moudon, Anne Vernez; Doescher, Mark P.

2016-01-01

Built environment (BE) data in geographic information system (GIS) format are increasingly available from public agencies and private providers. These data can provide objective, low-cost BE data over large regions and are often used in public health research and surveillance. Yet challenges exist in repurposing GIS data for health research. The GIS data do not always capture desired constructs; the data can be of varying quality and completeness; and the data definitions, structures, and spatial representations are often inconsistent across sources. Using the Small Town Walkability study as an illustration, we describe (a) the range of BE characteristics measurable in a GIS that may be associated with active living, (b) the availability of these data across nine U.S. small towns, (c) inconsistencies in the GIS BE data that were available, and (d) strategies for developing accurate, complete, and consistent GIS BE data appropriate for research. Based on a conceptual framework and existing literature, objectively measurable characteristics of the BE potentially related to active living were classified under nine domains: generalized land uses, morphology, density, destinations, transportation system, traffic conditions, neighborhood behavioral conditions, economic environment, and regional location. At least some secondary GIS data were available across all nine towns for seven of the nine BE domains. Data representing high-resolution or behavioral aspects of the BE were often not available. Available GIS BE data - especially tax parcel data - often contained varying attributes and levels of detail across sources. When GIS BE data were available from multiple sources, the accuracy, completeness, and consistency of the data could be reasonable ensured for use in research. But this required careful attention to the definition and spatial representation of the BE characteristic of interest. Manipulation of the secondary source data was often required, which was facilitated through protocols. PMID:28459001

Secondary GIS built environment data for health research: guidance for data development.

PubMed

Stewart, Orion T; Carlos, Heather A; Lee, Chanam; Berke, Ethan M; Hurvitz, Philip M; Li, Li; Moudon, Anne Vernez; Doescher, Mark P

2016-12-01

Built environment (BE) data in geographic information system (GIS) format are increasingly available from public agencies and private providers. These data can provide objective, low-cost BE data over large regions and are often used in public health research and surveillance. Yet challenges exist in repurposing GIS data for health research. The GIS data do not always capture desired constructs; the data can be of varying quality and completeness; and the data definitions, structures, and spatial representations are often inconsistent across sources. Using the Small Town Walkability study as an illustration, we describe (a) the range of BE characteristics measurable in a GIS that may be associated with active living, (b) the availability of these data across nine U.S. small towns, (c) inconsistencies in the GIS BE data that were available, and (d) strategies for developing accurate, complete, and consistent GIS BE data appropriate for research. Based on a conceptual framework and existing literature, objectively measurable characteristics of the BE potentially related to active living were classified under nine domains: generalized land uses, morphology, density, destinations, transportation system, traffic conditions, neighborhood behavioral conditions, economic environment, and regional location. At least some secondary GIS data were available across all nine towns for seven of the nine BE domains. Data representing high-resolution or behavioral aspects of the BE were often not available. Available GIS BE data - especially tax parcel data - often contained varying attributes and levels of detail across sources. When GIS BE data were available from multiple sources, the accuracy, completeness, and consistency of the data could be reasonable ensured for use in research. But this required careful attention to the definition and spatial representation of the BE characteristic of interest. Manipulation of the secondary source data was often required, which was facilitated through protocols.

Sustainability of outdoor school ground smoking bans at secondary schools: a mixed-method study.

PubMed

Rozema, A D; Mathijssen, J J P; Jansen, M W J; van Oers, J A M

2018-02-01

Although increasing numbers of countries are implementing outdoor school ground smoking bans at secondary schools, less attention is paid to the post-implementation period even though sustainability of a policy is essential for long-term effectiveness. Therefore, this study assesses the level of sustainability and examines perceived barriers/facilitators related to the sustainability of an outdoor school ground smoking ban at secondary schools. A mixed-method design was used with a sequential explanatory approach. In phase I, 438 online surveys were conducted and in phase II, 15 semi-structured interviews were obtained from directors of relevant schools. ANOVA (phase I) and a thematic approach (phase II) were used to analyze data. Level of sustainability of an outdoor school ground smoking ban was high at the 48% Dutch schools with an outdoor smoking ban. Furthermore, school size was significantly associated with sustainability. The perceived barriers/facilitators fell into three categories: (i) smoking ban implementation factors (side-effects, enforcement, communication, guidelines and collaboration), (ii) school factors (physical environment, school culture, education type and school policy) and (iii) community environment factors (legislation and social environment). Internationally, the spread of outdoor school ground smoking bans could be further promoted. Once implemented, the ban has become 'normal' practice and investments tend to endure. Moreover, involvement of all staff is important for sustainability as they function as role models, have an interrelationship with students, and share responsibility for enforcement. These findings are promising for the sustainability of future tobacco control initiatives to further protect against the morbidity/mortality associated with smoking. © The Author 2017. Published by Oxford University Press on behalf of the European Public Health Association.

Role of DNA secondary structures in fragile site breakage along human chromosome 10

PubMed Central

Dillon, Laura W.; Pierce, Levi C. T.; Ng, Maggie C. Y.; Wang, Yuh-Hwa

2013-01-01

The formation of alternative DNA secondary structures can result in DNA breakage leading to cancer and other diseases. Chromosomal fragile sites, which are regions of the genome that exhibit chromosomal breakage under conditions of mild replication stress, are predicted to form stable DNA secondary structures. DNA breakage at fragile sites is associated with regions that are deleted, amplified or rearranged in cancer. Despite the correlation, unbiased examination of the ability to form secondary structures has not been evaluated in fragile sites. Here, using the Mfold program, we predict potential DNA secondary structure formation on the human chromosome 10 sequence, and utilize this analysis to compare fragile and non-fragile DNA. We found that aphidicolin (APH)-induced common fragile sites contain more sequence segments with potential high secondary structure-forming ability, and these segments clustered more densely than those in non-fragile DNA. Additionally, using a threshold of secondary structure-forming ability, we refined legitimate fragile sites within the cytogenetically defined boundaries, and identified potential fragile regions within non-fragile DNA. In vitro detection of alternative DNA structure formation and a DNA breakage cell assay were used to validate the computational predictions. Many of the regions identified by our analysis coincide with genes mutated in various diseases and regions of copy number alteration in cancer. This study supports the role of DNA secondary structures in common fragile site instability, provides a systematic method for their identification and suggests a mechanism by which DNA secondary structures can lead to human disease. PMID:23297364

Influence of selected physicochemical parameters on microbiological activity of mucks.

NASA Astrophysics Data System (ADS)

Całka, A.; Sokołowska, Z.; Warchulska, P.; Dąbek-Szreniawska, M.

2009-04-01

One of the basic factor decided about soil fertility are microorganisms that together with flora, determine trend and character of biochemical processes as well totality of fundamental transformations connected with biogeochemistry and physicochemical properties of soil. Determination of general bacteria number, quantity of selected groups of microorganisms and investigation of respiration intensity let estimate microbiological activity of soil. Intensity of microbiological processes is directly connected with physicochemical soil parameters. In that case, such structural parameters as bulk density, porosity, surface or carbon content play significant role. Microbiological activity also changes within the bounds of mucks with different stage of humification and secondary transformation. Knowledge of relations between structural properties, microorganism activity and degree of transformation and humification can lead to better understanding microbiological processes as well enable to estimate microbiological activity at given physicochemical conditions and at progressing process of soil transformation. The study was carried out on two peaty-moorsh (muck) soils at different state of secondary transformation and humification degree. Soil samples were collected from Polesie Lubelskie (layer depth: 5 - 25 cm). Investigated mucks originated from soils formed from low peatbogs. Soil sample marked as I belonged to muck group weakly secondary transformed. Second sample (II) represented soil group with middle stage of secondary transformation. The main purpose of the research was to examine the relations between some physicochemical and surface properties and their biological activity. Total number and respiration activity of microorganisms were determined. The effectiveness of utilizing the carbon substances from the soil by the bacteria increased simultaneously with the transformation state of the peat-muck soils. Quantity of organic carbon decreased distinctly in the soil at the higher stage of secondary transformation and it influenced quantity and activity of soil microorganisms. Bulk density and surface increased with increasing secondary transformation degree. On the other hand, porosity decreased with increasing secondary transformation index. Process of secondary transformation influenced the soil environment for the microbes by changing the physicochemical properties. This way it influenced the number of microorganisms and caused changes of biological activity in the soils.

40 CFR 267.1104 - How may I obtain a waiver from secondary containment requirements?

Code of Federal Regulations, 2010 CFR

2010-07-01

... suppression liquids required to meet occupational health and safety requirements, and (b) Containment of... 40 Protection of Environment 26 2010-07-01 2010-07-01 false How may I obtain a waiver from secondary containment requirements? 267.1104 Section 267.1104 Protection of Environment ENVIRONMENTAL...

40 CFR 267.1104 - How may I obtain a waiver from secondary containment requirements?

Code of Federal Regulations, 2013 CFR

2013-07-01

... suppression liquids required to meet occupational health and safety requirements, and (b) Containment of... 40 Protection of Environment 28 2013-07-01 2013-07-01 false How may I obtain a waiver from secondary containment requirements? 267.1104 Section 267.1104 Protection of Environment ENVIRONMENTAL...

40 CFR 267.1104 - How may I obtain a waiver from secondary containment requirements?

Code of Federal Regulations, 2012 CFR

2012-07-01

... suppression liquids required to meet occupational health and safety requirements, and (b) Containment of... 40 Protection of Environment 28 2012-07-01 2012-07-01 false How may I obtain a waiver from secondary containment requirements? 267.1104 Section 267.1104 Protection of Environment ENVIRONMENTAL...

40 CFR 267.1104 - How may I obtain a waiver from secondary containment requirements?

Code of Federal Regulations, 2011 CFR

2011-07-01

... suppression liquids required to meet occupational health and safety requirements, and (b) Containment of... 40 Protection of Environment 27 2011-07-01 2011-07-01 false How may I obtain a waiver from secondary containment requirements? 267.1104 Section 267.1104 Protection of Environment ENVIRONMENTAL...

Spaces for Learning: Development and Validation of the School Physical and Campus Environment Survey

ERIC Educational Resources Information Center

Zandvliet, David; Broekhuizen, Avril

2017-01-01

The study of learning environments involves describing educational contexts and identifying empirical relationships among subject matter (curriculum), teaching practices and other environmental variables. In recent years, this has become a growing field of academic inquiry within elementary, secondary and post-secondary research. Investigations of…

Building a knowledge-based statistical potential by capturing high-order inter-residue interactions and its applications in protein secondary structure assessment.

PubMed

Li, Yaohang; Liu, Hui; Rata, Ionel; Jakobsson, Eric

2013-02-25

The rapidly increasing number of protein crystal structures available in the Protein Data Bank (PDB) has naturally made statistical analyses feasible in studying complex high-order inter-residue correlations. In this paper, we report a context-based secondary structure potential (CSSP) for assessing the quality of predicted protein secondary structures generated by various prediction servers. CSSP is a sequence-position-specific knowledge-based potential generated based on the potentials of mean force approach, where high-order inter-residue interactions are taken into consideration. The CSSP potential is effective in identifying secondary structure predictions with good quality. In 56% of the targets in the CB513 benchmark, the optimal CSSP potential is able to recognize the native secondary structure or a prediction with Q3 accuracy higher than 90% as best scored in the predicted secondary structures generated by 10 popularly used secondary structure prediction servers. In more than 80% of the CB513 targets, the predicted secondary structures with the lowest CSSP potential values yield higher than 80% Q3 accuracy. Similar performance of CSSP is found on the CASP9 targets as well. Moreover, our computational results also show that the CSSP potential using triplets outperforms the CSSP potential using doublets and is currently better than the CSSP potential using quartets.

A Qualitative Study of the Work Environments of Mexican Nurses

PubMed Central

Squires, Allison; Juarez, Adrian

2012-01-01

Background Studies of the nursing work environment are increasingly common in developed countries, but few exist in developing countries. Because of resource differences between the two contexts, researchers need to clarify what aspects of the work environments are similar and different. Objectives To study the perspectives of Mexican nurses about their work environments to determine similarities and differences to results from developed world studies. Design A secondary, directed content analysis of qualitative data from 46 Spanish language interviews using workplace-oriented themes Setting Purposively selected Mexican states from four regions of the country that reflect the country’s socioeconomic differences. Participants Practicing Mexican nurses with at least one year of clinical experience and currently working in nursing. Participants were recruited through convenience and snowball sampling techniques. Methods Initial data collection occurred in 2006 and 2008 during a broader study about professionalization processes that occurred in Mexican nursing between 1980 and 2005. The secondary, directed content analysis focused on an in-depth exploration of a central theme that emerged from the two original studies: The Workplace. The directed content analysis used themes from the global nursing work environment literature to structure the analysis: Professional relationships, organizational administrative practices, and quality of care and services. Results The three themes from the global literature were relevant for the Mexican context and a new one emerged related to hiring practices. By category, the same factors that created positive or negative perceptions of the work environment matched findings from other international studies conducted in developed countries. The descriptors of the category, however, had different conceptual meanings that illustrate the health system challenges in Mexico. Conclusions Findings from this study suggest that studies that seek to measure nursing work environments will most likely apply in Mexico and other Latin American or middle-income countries. Instruments designed to measure the work environment of nurses in these countries may prove relevant in those contexts, but require careful adaptation and systematic translations to ensure it. PMID:22386989

The role of extremophile in the redox reaction of Fe and As relating with the formation of secondary phase mineral in extreme environment, Norris Geyser Basin, Yellowstone National Park, USA

NASA Astrophysics Data System (ADS)

Koo, T. H.; Kim, J. Y.; Park, K. R.; Jung, D. H.; Geesey, G. G.; Kim, J. W.

2015-12-01

Redox reaction associated with microbial elemental respiration is a ubiquitous process in sediments and suspended particles at various temperatures or pH/Eh conditions. Particularly, changes in elemental redox states (structural or dissolved elemental form) induced by microbial respiration result in the unexpected biogeochemical reactions in the light of biotic/abiotic mineralization. The objective of the present study is, therefore to investigate the secondary phase mineralization through a-/biogeochemical Fe and As redox cycling in the acido-hyperhtermal Norris Geyser Basin (NGB) in Yellowstone National Park, USA, typical of the extreme condition. X-ray diffraction, scanning electron microscope with energy dispersive x-ray spectroscopy, X-ray absorption near edge structure, inductively coupled plasma-atomic emission spectrometer and liquid chromatography with ICP-mass spectroscopy with filtrated supernatant were performed for the mineralogical and hydro-geochemical analysis. The clay slurry collected from the active hot-spring of the NGB area (pH=3.5 and Temperature=78 ℃) was incubated with ("enrichment") or without the growth medium ("natural"). The control was prepared in the same condition except adding the glutaraldehyde to eliminate the microbial activity. The secondary phase mineral formation of the oxidative phase of Fe and As, and K identified as 'Pharmacosiderite' only appeared in the enrichment set suggesting a role of extremophiles in the mineral formation. The considerable population of Fe-oxidizer (Metallosphera yellowstonensis MK-1) and As-oxidizer (Sulfurihydrogenibium sp.) was measured by phylogenetic analysis in the present study area. The inhibition of As-oxidation in the low pH conditions was reported in the previous study, however the As-redox reaction was observed and consequently, precipitated the Pharmacosiderite only in the enrichment set suggesting a biotic mineralization. The present study collectively suggests that the microbial activity may bypass the chemical or thermodynamical reaction barriers and promote the secondary phase mineral formation through the elemental respiration. The possible biotic/abiotic mechanism or process in mineral alteration/formation in extreme environment will be discussed.

40 CFR 421.30 - Applicability: Description of the secondary aluminum smelting subcategory.

Code of Federal Regulations, 2010 CFR

2010-07-01

... secondary aluminum smelting subcategory. 421.30 Section 421.30 Protection of Environment ENVIRONMENTAL... CATEGORY Secondary Aluminum Smelting Subcategory § 421.30 Applicability: Description of the secondary aluminum smelting subcategory. The provisions of this subpart are applicable to discharges resulting from...

Validity of Secondary Retail Food Outlet Data

PubMed Central

Fleischhacker, Sheila E.; Evenson, Kelly R.; Sharkey, Joseph; Pitts, Stephanie B.J.; Rodriguez, Daniel A.

2013-01-01

Context Improving access to healthy foods is a promising strategy to prevent nutrition-related chronic diseases. To characterize retail food environments and identify areas with limited retail access, researchers, government programs, and community advocates have primarily used secondary retail food outlet data sources (e.g., InfoUSA or government food registries). To advance the state of the science on measuring retail food environments, this systematic review examined the evidence for validity reported for secondary retail food outlet data sources for characterizing retail food environments. Evidence acquisition A literature search was conducted through December 31, 2012 to identify peer-reviewed published literature that compared secondary retail food outlet data sources to primary data sources (i.e., field observations) for accuracy of identifying the type and location of retail food outlets. Data were analyzed in 2013. Evidence synthesis Nineteen studies met the inclusion criteria. The evidence for validity reported varied by secondary data sources examined, primary data–gathering approaches, retail food outlets examined, and geographic and sociodemographic characteristics. More than half of the studies (53%) did not report evidence for validity by type of food outlet examined and by a particular secondary data source. Conclusions Researchers should strive to gather primary data but if relying on secondary data sources, InfoUSA and government food registries had higher levels of agreement than reported by other secondary data sources and may provide sufficient accuracy for exploring these associations in large study areas. PMID:24050423

R-chie: a web server and R package for visualizing RNA secondary structures

PubMed Central

Lai, Daniel; Proctor, Jeff R.; Zhu, Jing Yun A.; Meyer, Irmtraud M.

2012-01-01

Visually examining RNA structures can greatly aid in understanding their potential functional roles and in evaluating the performance of structure prediction algorithms. As many functional roles of RNA structures can already be studied given the secondary structure of the RNA, various methods have been devised for visualizing RNA secondary structures. Most of these methods depict a given RNA secondary structure as a planar graph consisting of base-paired stems interconnected by roundish loops. In this article, we present an alternative method of depicting RNA secondary structure as arc diagrams. This is well suited for structures that are difficult or impossible to represent as planar stem-loop diagrams. Arc diagrams can intuitively display pseudo-knotted structures, as well as transient and alternative structural features. In addition, they facilitate the comparison of known and predicted RNA secondary structures. An added benefit is that structure information can be displayed in conjunction with a corresponding multiple sequence alignments, thereby highlighting structure and primary sequence conservation and variation. We have implemented the visualization algorithm as a web server R-chie as well as a corresponding R package called R4RNA, which allows users to run the software locally and across a range of common operating systems. PMID:22434875

Characterising RNA secondary structure space using information entropy

PubMed Central

2013-01-01

Comparative methods for RNA secondary structure prediction use evolutionary information from RNA alignments to increase prediction accuracy. The model is often described in terms of stochastic context-free grammars (SCFGs), which generate a probability distribution over secondary structures. It is, however, unclear how this probability distribution changes as a function of the input alignment. As prediction programs typically only return a single secondary structure, better characterisation of the underlying probability space of RNA secondary structures is of great interest. In this work, we show how to efficiently compute the information entropy of the probability distribution over RNA secondary structures produced for RNA alignments by a phylo-SCFG, and implement it for the PPfold model. We also discuss interpretations and applications of this quantity, including how it can clarify reasons for low prediction reliability scores. PPfold and its source code are available from http://birc.au.dk/software/ppfold/. PMID:23368905

Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy

PubMed Central

Garmann, Rees F.; Gopal, Ajaykumar; Athavale, Shreyas S.; Knobler, Charles M.; Gelbart, William M.; Harvey, Stephen C.

2015-01-01

The lifecycle, and therefore the virulence, of single-stranded (ss)-RNA viruses is regulated not only by their particular protein gene products, but also by the secondary and tertiary structure of their genomes. The secondary structure of the entire genomic RNA of satellite tobacco mosaic virus (STMV) was recently determined by selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE). The SHAPE analysis suggested a single highly extended secondary structure with much less branching than occurs in the ensemble of structures predicted by purely thermodynamic algorithms. Here we examine the solution-equilibrated STMV genome by direct visualization with cryo-electron microscopy (cryo-EM), using an RNA of similar length transcribed from the yeast genome as a control. The cryo-EM data reveal an ensemble of branching patterns that are collectively consistent with the SHAPE-derived secondary structure model. Thus, our results both elucidate the statistical nature of the secondary structure of large ss-RNAs and give visual support for modern RNA structure determination methods. Additionally, this work introduces cryo-EM as a means to distinguish between competing secondary structure models if the models differ significantly in terms of the number and/or length of branches. Furthermore, with the latest advances in cryo-EM technology, we suggest the possibility of developing methods that incorporate restraints from cryo-EM into the next generation of algorithms for the determination of RNA secondary and tertiary structures. PMID:25752599

BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra.

PubMed

Micsonai, András; Wien, Frank; Bulyáki, Éva; Kun, Judit; Moussong, Éva; Lee, Young-Ho; Goto, Yuji; Réfrégiers, Matthieu; Kardos, József

2018-06-11

Circular dichroism (CD) spectroscopy is a widely used method to study the protein secondary structure. However, for decades, the general opinion was that the correct estimation of β-sheet content is challenging because of the large spectral and structural diversity of β-sheets. Recently, we showed that the orientation and twisting of β-sheets account for the observed spectral diversity, and developed a new method to estimate accurately the secondary structure (PNAS, 112, E3095). BeStSel web server provides the Beta Structure Selection method to analyze the CD spectra recorded by conventional or synchrotron radiation CD equipment. Both normalized and measured data can be uploaded to the server either as a single spectrum or series of spectra. The originality of BeStSel is that it carries out a detailed secondary structure analysis providing information on eight secondary structure components including parallel-β structure and antiparallel β-sheets with three different groups of twist. Based on these, it predicts the protein fold down to the topology/homology level of the CATH protein fold classification. The server also provides a module to analyze the structures deposited in the PDB for BeStSel secondary structure contents in relation to Dictionary of Secondary Structure of Proteins data. The BeStSel server is freely accessible at http://bestsel.elte.hu.

40 CFR 421.290 - Applicability: Description of the secondary tin subcategory.

Code of Federal Regulations, 2012 CFR

2012-07-01

... secondary tin subcategory. 421.290 Section 421.290 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Tin Subcategory § 421.290 Applicability: Description of the secondary tin subcategory. The provisions of this subpart are applicable to discharges resulting from the production of tin at secondary tin...

40 CFR 421.290 - Applicability: Description of the secondary tin subcategory.

Code of Federal Regulations, 2010 CFR

2010-07-01

... secondary tin subcategory. 421.290 Section 421.290 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Tin Subcategory § 421.290 Applicability: Description of the secondary tin subcategory. The provisions of this subpart are applicable to discharges resulting from the production of tin at secondary tin...

40 CFR 421.290 - Applicability: Description of the secondary tin subcategory.

Code of Federal Regulations, 2013 CFR

2013-07-01

... secondary tin subcategory. 421.290 Section 421.290 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Tin Subcategory § 421.290 Applicability: Description of the secondary tin subcategory. The provisions of this subpart are applicable to discharges resulting from the production of tin at secondary tin...

40 CFR 421.290 - Applicability: Description of the secondary tin subcategory.

Code of Federal Regulations, 2011 CFR

2011-07-01

... secondary tin subcategory. 421.290 Section 421.290 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Tin Subcategory § 421.290 Applicability: Description of the secondary tin subcategory. The provisions of this subpart are applicable to discharges resulting from the production of tin at secondary tin...

40 CFR 421.290 - Applicability: Description of the secondary tin subcategory.

Code of Federal Regulations, 2014 CFR

2014-07-01

... secondary tin subcategory. 421.290 Section 421.290 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Tin Subcategory § 421.290 Applicability: Description of the secondary tin subcategory. The provisions of this subpart are applicable to discharges resulting from the production of tin at secondary tin...

40 CFR 421.300 - Applicability: Description of the primary and secondary titanium subcategory.

Code of Federal Regulations, 2010 CFR

2010-07-01

... primary and secondary titanium subcategory. 421.300 Section 421.300 Protection of Environment... POINT SOURCE CATEGORY Primary and Secondary Titanium Subcategory § 421.300 Applicability: Description of the primary and secondary titanium subcategory. The provisions of this subpart are applicable to...

40 CFR 421.300 - Applicability: Description of the primary and secondary titanium subcategory.

Code of Federal Regulations, 2012 CFR

2012-07-01

... primary and secondary titanium subcategory. 421.300 Section 421.300 Protection of Environment... POINT SOURCE CATEGORY Primary and Secondary Titanium Subcategory § 421.300 Applicability: Description of the primary and secondary titanium subcategory. The provisions of this subpart are applicable to...

40 CFR 421.300 - Applicability: Description of the primary and secondary titanium subcategory.

Code of Federal Regulations, 2013 CFR

2013-07-01

... primary and secondary titanium subcategory. 421.300 Section 421.300 Protection of Environment... POINT SOURCE CATEGORY Primary and Secondary Titanium Subcategory § 421.300 Applicability: Description of the primary and secondary titanium subcategory. The provisions of this subpart are applicable to...

40 CFR 421.300 - Applicability: Description of the primary and secondary titanium subcategory.

Code of Federal Regulations, 2011 CFR

2011-07-01

... primary and secondary titanium subcategory. 421.300 Section 421.300 Protection of Environment... POINT SOURCE CATEGORY Primary and Secondary Titanium Subcategory § 421.300 Applicability: Description of the primary and secondary titanium subcategory. The provisions of this subpart are applicable to...

40 CFR 421.300 - Applicability: Description of the primary and secondary titanium subcategory.

Code of Federal Regulations, 2014 CFR

2014-07-01

... primary and secondary titanium subcategory. 421.300 Section 421.300 Protection of Environment... POINT SOURCE CATEGORY Primary and Secondary Titanium Subcategory § 421.300 Applicability: Description of the primary and secondary titanium subcategory. The provisions of this subpart are applicable to...

40 CFR 421.60 - Applicability: Description of the secondary copper subcategory.

Code of Federal Regulations, 2011 CFR

2011-07-01

... secondary copper subcategory. 421.60 Section 421.60 Protection of Environment ENVIRONMENTAL PROTECTION... CATEGORY Secondary Copper Subcategory § 421.60 Applicability: Description of the secondary copper..., processing, and remelting of new and used copper scrap and residues to produce copper metal and copper alloys...

40 CFR 421.60 - Applicability: Description of the secondary copper subcategory.

Code of Federal Regulations, 2010 CFR

2010-07-01

... secondary copper subcategory. 421.60 Section 421.60 Protection of Environment ENVIRONMENTAL PROTECTION... CATEGORY Secondary Copper Subcategory § 421.60 Applicability: Description of the secondary copper..., processing, and remelting of new and used copper scrap and residues to produce copper metal and copper alloys...

40 CFR 421.130 - Applicability: Description of the secondary lead subcategory.

Code of Federal Regulations, 2012 CFR

2012-07-01

... secondary lead subcategory. 421.130 Section 421.130 Protection of Environment ENVIRONMENTAL PROTECTION... CATEGORY Secondary Lead Subcategory § 421.130 Applicability: Description of the secondary lead subcategory. The provisions of this subpart are applicable to discharges resulting from the production of lead by...

40 CFR 421.130 - Applicability: Description of the secondary lead subcategory.

Code of Federal Regulations, 2011 CFR

2011-07-01

... secondary lead subcategory. 421.130 Section 421.130 Protection of Environment ENVIRONMENTAL PROTECTION... CATEGORY Secondary Lead Subcategory § 421.130 Applicability: Description of the secondary lead subcategory. The provisions of this subpart are applicable to discharges resulting from the production of lead by...

40 CFR 421.130 - Applicability: Description of the secondary lead subcategory.

Code of Federal Regulations, 2014 CFR

2014-07-01

... secondary lead subcategory. 421.130 Section 421.130 Protection of Environment ENVIRONMENTAL PROTECTION... CATEGORY Secondary Lead Subcategory § 421.130 Applicability: Description of the secondary lead subcategory. The provisions of this subpart are applicable to discharges resulting from the production of lead by...

40 CFR 421.130 - Applicability: Description of the secondary lead subcategory.

Code of Federal Regulations, 2013 CFR

2013-07-01

... secondary lead subcategory. 421.130 Section 421.130 Protection of Environment ENVIRONMENTAL PROTECTION... CATEGORY Secondary Lead Subcategory § 421.130 Applicability: Description of the secondary lead subcategory. The provisions of this subpart are applicable to discharges resulting from the production of lead by...

40 CFR 421.130 - Applicability: Description of the secondary lead subcategory.

Code of Federal Regulations, 2010 CFR

2010-07-01

... secondary lead subcategory. 421.130 Section 421.130 Protection of Environment ENVIRONMENTAL PROTECTION... CATEGORY Secondary Lead Subcategory § 421.130 Applicability: Description of the secondary lead subcategory. The provisions of this subpart are applicable to discharges resulting from the production of lead by...

Structurally coloured secondary particles composed of black and white colloidal particles.

PubMed

Takeoka, Yukikazu; Yoshioka, Shinya; Teshima, Midori; Takano, Atsushi; Harun-Ur-Rashid, Mohammad; Seki, Takahiro

2013-01-01

This study investigated the colourful secondary particles formed by controlling the aggregation states of colloidal silica particles and the enhancement of the structural colouration of the secondary particles caused by adding black particles. We obtained glossy, partially structurally coloured secondary particles in the absence of NaCl, but matte, whitish secondary particles were obtained in the presence of NaCl. When a small amount of carbon black was incorporated into both types of secondary particles, the incoherent multiple scattering of light from the amorphous region was considerably reduced. However, the peak intensities in the reflection spectra, caused by Bragg reflection and by coherent single wavelength scattering, were only slightly decreased. Consequently, a brighter structural colour of these secondary particles was observed with the naked eye. Furthermore, when magnetite was added as a black particle, the coloured secondary particles could be moved and collected by applying an external magnetic field.

Structurally Coloured Secondary Particles Composed of Black and White Colloidal Particles

PubMed Central

Takeoka, Yukikazu; Yoshioka, Shinya; Teshima, Midori; Takano, Atsushi; Harun-Ur-Rashid, Mohammad; Seki, Takahiro

2013-01-01

This study investigated the colourful secondary particles formed by controlling the aggregation states of colloidal silica particles and the enhancement of the structural colouration of the secondary particles caused by adding black particles. We obtained glossy, partially structurally coloured secondary particles in the absence of NaCl, but matte, whitish secondary particles were obtained in the presence of NaCl. When a small amount of carbon black was incorporated into both types of secondary particles, the incoherent multiple scattering of light from the amorphous region was considerably reduced. However, the peak intensities in the reflection spectra, caused by Bragg reflection and by coherent single wavelength scattering, were only slightly decreased. Consequently, a brighter structural colour of these secondary particles was observed with the naked eye. Furthermore, when magnetite was added as a black particle, the coloured secondary particles could be moved and collected by applying an external magnetic field. PMID:23917891

Analysis of protein circular dichroism spectra for secondary structure using a simple matrix multiplication.

PubMed

Compton, L A; Johnson, W C

1986-05-15

Inverse circular dichroism (CD) spectra are presented for each of the five major secondary structures of proteins: alpha-helix, antiparallel and parallel beta-sheet, beta-turn, and other (random) structures. The fraction of the each secondary structure in a protein is predicted by forming the dot product of the corresponding inverse CD spectrum, expressed as a vector, with the CD spectrum of the protein digitized in the same way. We show how this method is based on the construction of the generalized inverse from the singular value decomposition of a set of CD spectra corresponding to proteins whose secondary structures are known from X-ray crystallography. These inverse spectra compute secondary structure directly from protein CD spectra without resorting to least-squares fitting and standard matrix inversion techniques. In addition, spectra corresponding to the individual secondary structures, analogous to the CD spectra of synthetic polypeptides, are generated from the five most significant CD eigenvectors.

Enhanced protein retention on poly(caprolactone) via surface initiated polymerization of acrylamide

NASA Astrophysics Data System (ADS)

Ma, Yuhao; Cai, Mengtan; He, Liu; Luo, Xianglin

2016-01-01

To enhance the biocompatibility or extend the biomedical application of poly(caprolactone) (PCL), protein retention on PCL surface is often required. In this study, poly(acrylamide) (PAAm) brushes were grown from PCL surface via surface-initiated atom transfer radical polymerization (SI-ATRP) and served as a protein-capturing platform. Grafted PAAm was densely packed on surface and exhibited superior protein retention ability. Captured protein was found to be resistant to washing under detergent environment. Furthermore, protein structure after being captured was investigated by circular dichroism (CD) spectroscopy, and the CD spectra verified that secondary structure of captured proteins was maintained, indicating no denaturation of protein happened for retention process.

A statistical learning approach to the modeling of chromatographic retention of oligonucleotides incorporating sequence and secondary structure data

PubMed Central

Sturm, Marc; Quinten, Sascha; Huber, Christian G.; Kohlbacher, Oliver

2007-01-01

We propose a new model for predicting the retention time of oligonucleotides. The model is based on ν support vector regression using features derived from base sequence and predicted secondary structure of oligonucleotides. Because of the secondary structure information, the model is applicable even at relatively low temperatures where the secondary structure is not suppressed by thermal denaturing. This makes the prediction of oligonucleotide retention time for arbitrary temperatures possible, provided that the target temperature lies within the temperature range of the training data. We describe different possibilities of feature calculation from base sequence and secondary structure, present the results and compare our model to existing models. PMID:17567619

Microstructure and phase composition characterization in a Co{sub 38}Ni{sub 33}Al{sub 29} ferromagnetic shape memory alloy

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

Lu, J.B.

2016-08-15

Transmission electron microscopy was performed to investigate the microstructures of a secondary phase and its surrounding matrix in a Co{sub 38}Ni{sub 33}Al{sub 29} ferromagnetic shape memory alloy. The secondary phase shows a γ′ L1{sub 2} structure exhibiting a dendritic morphology with enclosed B2 austenite regions while the matrix shows the L1{sub 0} martensitic structure. A secondary phase-austenite-martensite sandwich structure with residual austenite ranging from several hundred nanometers to several micrometers wide is observed at the secondary phase-martensite interface due to the depletion of Co and enrichment of Al in the chemical gradient zone and the effect of the strong martensiticmore » start temperature dependency of the element concentrations. The crystallographic orientation relationship of the secondary phase and the B2 austenite fits the Kurdjumov-Sachs relationship. - Highlights: •The secondary phase has a γ′ L1{sub 2} structure exhibiting a dendritic morphology. •A secondary phase-austenite-martensite sandwich structure is observed. •The structural sandwich structure is due to elemental composition variation. •The secondary phase and the B2 austenite fit the Kurdjumov-Sachs relationship.« less

Merging Social Networking Environments and Formal Learning Environments to Support and Facilitate Interprofessional Instruction

PubMed Central

King, Sharla; Greidanus, Elaine; Carbonaro, Michael; Drummond, Jane; Patterson, Steven

2009-01-01

This study describes the redesign of an interprofessional team development course for health science students. A theoretical model is hypothesized as a framework for the redesign process, consisting of two themes: 1) the increasing trend among post-secondary students to participate in social networking (e.g., Facebook, Second Life) and 2) the need for healthcare educators to provide interprofessional training that results in effective communities of practice and better patient care. The redesign focused on increasing the relevance of the course through the integration of custom-designed technology to facilitate social networking during their interprofessional education. Results suggest that students in an educationally structured social networking environment can be guided to join learning communities quickly and access course materials. More research and implementation work is required to effectively develop interprofessional health sciences communities in a combined face-to-face and on-line social networking context. PMID:20165519

[Psychological theories of motivation].

PubMed

Quoniam, Nolwenn; Bungener, Catherine

2004-03-01

The comprehension of the principles guiding the human actions has always been an important aspect of philosophy. The development of experimental psychology first completely rejected all mental explanations such as will, intentions or motives. Behavior should then only be understood as determined by conditioning and learning. However, different theories denied that human behavior could be considered as purely reactive to the environment and stressed the active role of the organism on the environment. Theories from the humanist psychology and the social psychology described two kinds of motivation. The extrinsic motivation results from external stimuli and the intrinsic motivation from the organism himself. Our behavior is therefore determined by an interaction between our beliefs, expectations, needs and the environment. Actually, the concept of motivation is not well specified. It refers either to a global dynamic structure responsible for action either to a specific tendency toward some specific actions. Anyway, motivation is a concept infered from behavior. Therefore, its evaluation could only be secondary.

Merging social networking environments and formal learning environments to support and facilitate interprofessional instruction.

PubMed

King, Sharla; Greidanus, Elaine; Carbonaro, Michael; Drummond, Jane; Patterson, Steven

2009-04-28

This study describes the redesign of an interprofessional team development course for health science students. A theoretical model is hypothesized as a framework for the redesign process, consisting of two themes: 1) the increasing trend among post-secondary students to participate in social networking (e.g., Facebook, Second Life) and 2) the need for healthcare educators to provide interprofessional training that results in effective communities of practice and better patient care. The redesign focused on increasing the relevance of the course through the integration of custom-designed technology to facilitate social networking during their interprofessional education. Results suggest that students in an educationally structured social networking environment can be guided to join learning communities quickly and access course materials. More research and implementation work is required to effectively develop interprofessional health sciences communities in a combined face-to-face and on-line social networking context.

Structure Prediction of the Second Extracellular Loop in G-Protein-Coupled Receptors

PubMed Central

Kmiecik, Sebastian; Jamroz, Michal; Kolinski, Michal

2014-01-01

G-protein-coupled receptors (GPCRs) play key roles in living organisms. Therefore, it is important to determine their functional structures. The second extracellular loop (ECL2) is a functionally important region of GPCRs, which poses significant challenge for computational structure prediction methods. In this work, we evaluated CABS, a well-established protein modeling tool for predicting ECL2 structure in 13 GPCRs. The ECL2s (with between 13 and 34 residues) are predicted in an environment of other extracellular loops being fully flexible and the transmembrane domain fixed in its x-ray conformation. The modeling procedure used theoretical predictions of ECL2 secondary structure and experimental constraints on disulfide bridges. Our approach yielded ensembles of low-energy conformers and the most populated conformers that contained models close to the available x-ray structures. The level of similarity between the predicted models and x-ray structures is comparable to that of other state-of-the-art computational methods. Our results extend other studies by including newly crystallized GPCRs. PMID:24896119

The turn of the screw: an exercise in protein secondary structure.

PubMed

Pikaart, Michael

2011-01-01

An exercise using simple paper strips to illustrate protein helical and sheet secondary structures is presented. Drawing on the rich historical context of the use of physical models in protein biochemistry by early practitioners, in particular Linus Pauling, the purpose of this activity is to cultivate in students a hands-on, intuitive sense of protein secondary structure and to complement the common computer-based structural portrayals often used in teaching biochemistry. As students fold these paper strips into model secondary structures, they will better grasp how intramolecular hydrogen bonds form in the folding of a polypeptide into secondary structure, and how these hydrogen bonds direct the overall shape of helical and sheet structures, including the handedness of the α-helix and the difference between right- and the left-handed twist. Copyright © 2010 Wiley Periodicals, Inc.

VMD-SS: A graphical user interface plug-in to calculate the protein secondary structure in VMD program.

PubMed

Yahyavi, Masoumeh; Falsafi-Zadeh, Sajad; Karimi, Zahra; Kalatarian, Giti; Galehdari, Hamid

2014-01-01

The investigation on the types of secondary structure (SS) of a protein is important. The evolution of secondary structures during molecular dynamics simulations is a useful parameter to analyze protein structures. Therefore, it is of interest to describe VMD-SS (a software program) for the identification of secondary structure elements and its trajectories during simulation for known structures available at the Protein Data Bank (PDB). The program helps to calculate (1) percentage SS, (2) SS occurrence in each residue, (3) percentage SS during simulation, and (4) percentage residues in all SS types during simulation. The VMD-SS plug-in was designed using TCL script and stride to calculate secondary structure features. The database is available for free at http://science.scu.ac.ir/HomePage.aspx?TabID=13755.

Preferential melting of secondary structures during protein unfolding in different solvents: Competition between hydrophobic solvation and hydrogen bonding

NASA Astrophysics Data System (ADS)

Bagchi, Biman; Roy, Susmita; Ghosh, Rikhia

2014-03-01

Aqueous binary mixtures such as water-DMSO, water-urea, and water-ethanol are known to serve as denaturants of a host of proteins, although the detailed mechanism is often not known. Here we combine studies on several proteins in multiple binary mixtures to obtain a unified understanding of the phenomenon. We compare with experiments to support the simulation findings. The proteins considered include (i) chicken villin head piece (HP-36), (ii) immunoglobulin binding protein G (GB1), (iii) myoglobin and (iv) lysozyme. We find that for amphiphilic solvents like DMSO, the hydrophobic groups and the strong hydrogen bonding ability of the >S =O oxygen atom act together to facilitate the unfolding. However, the hydrophilic solvents like urea, due to the presence of more hydrophilic ends (C =O and two NH2) has a high propensity of forming hydrogen bonds with the side-chain residues and backbone of beta-sheet than the same of alpha helix. Such diversity among the unfolding pathways of a given protein in different chemical environments is especially characterized by the preferential solvation of a particular secondary structure.

Antifungal potential of marine natural products.

PubMed

El-Hossary, Ebaa M; Cheng, Cheng; Hamed, Mostafa M; El-Sayed Hamed, Ashraf Nageeb; Ohlsen, Knut; Hentschel, Ute; Abdelmohsen, Usama Ramadan

2017-01-27

Fungal diseases represent an increasing threat to human health worldwide which in some cases might be associated with substantial morbidity and mortality. However, only few antifungal drugs are currently available for the treatment of life-threatening fungal infections. Furthermore, plant diseases caused by fungal pathogens represent a worldwide economic problem for the agriculture industry. The marine environment continues to provide structurally diverse and biologically active secondary metabolites, several of which have inspired the development of new classes of therapeutic agents. Among these secondary metabolites, several compounds with noteworthy antifungal activities have been isolated from marine microorganisms, invertebrates, and algae. During the last fifteen years, around 65% of marine natural products possessing antifungal activities have been isolated from sponges and bacteria. This review gives an overview of natural products from diverse marine organisms that have shown in vitro and/or in vivo potential as antifungal agents, with their mechanism of action whenever applicable. The natural products literature is covered from January 2000 until June 2015, and we are reporting the chemical structures together with their biological activities, as well as the isolation source. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Thermal Design and Analysis of the Optical Telescope Assembly for the Gondola for High Altitude Planetary Science

NASA Technical Reports Server (NTRS)

O'Connor, Brian; Brooks, Thomas

2017-01-01

The NASA Gondola for High Altitude Planetary Science (GHAPS) project is an effort to design, build, and fly a balloon-borne platform for planetary science missions. GHAPS observations will be in the 300 nm to 5 micron wavelength region covering UV, visible, and near-mid IR. The primary element of the project is the Optical Telescope Assembly (OTA). It is a one meter aperture narrow-field-of-view telescope that contains the primary and secondary mirrors, the support system/metering structure, a secondary mirror focusing system, baffles, and insulation. This paper presents the thermal design and analysis that has been done to support the design of the OTA. A major part of the thermal analysis was bounding the flight environment for the six potential Columbia Scientific Balloon Facility launch sites. These analyses were used to give input into the Structural Thermal Optical Performance (STOP) analysis of the telescope. Also the analysis was used to select heater sizes for the few OTA associated electronic components. Currently the telescope is scheduled to have its first flight in 2019.

Conformational study of melectin and antapin antimicrobial peptides in model membrane environments

NASA Astrophysics Data System (ADS)

Kocourková, Lucie; Novotná, Pavlína; Čujová, Sabína; Čeřovský, Václav; Urbanová, Marie; Setnička, Vladimír

2017-01-01

Antimicrobial peptides have long been considered as promising compounds against drug-resistant pathogens. In this work, we studied the secondary structure of antimicrobial peptides melectin and antapin using electronic (ECD) and vibrational circular dichroism (VCD) spectroscopies that are sensitive to peptide secondary structures. The results from quantitative ECD spectral evaluation by Dichroweb and CDNN program and from the qualitative evaluation of the VCD spectra were compared. The antimicrobial activity of the selected peptides depends on their ability to adopt an amphipathic α-helical conformation on the surface of the bacterial membrane. Hence, solutions of different zwitterionic and negatively charged liposomes and micelles were used to mimic the eukaryotic and bacterial biological membranes. The results show a significant content of α-helical conformation in the solutions of negatively charged liposomes mimicking the bacterial membrane, thus correlating with the antimicrobial activity of the studied peptides. On the other hand in the solutions of zwitterionic liposomes used as models of the eukaryotic membranes, the fraction of α-helical conformation was lower, which corresponds with their moderate hemolytic activity.

Conservation of mRNA secondary structures may filter out mutations in Escherichia coli evolution

PubMed Central

Chursov, Andrey; Frishman, Dmitrij; Shneider, Alexander

2013-01-01

Recent reports indicate that mutations in viral genomes tend to preserve RNA secondary structure, and those mutations that disrupt secondary structural elements may reduce gene expression levels, thereby serving as a functional knockout. In this article, we explore the conservation of secondary structures of mRNA coding regions, a previously unknown factor in bacterial evolution, by comparing the structural consequences of mutations in essential and nonessential Escherichia coli genes accumulated over 40 000 generations in the course of the ‘long-term evolution experiment’. We monitored the extent to which mutations influence minimum free energy (MFE) values, assuming that a substantial change in MFE is indicative of structural perturbation. Our principal finding is that purifying selection tends to eliminate those mutations in essential genes that lead to greater changes of MFE values and, therefore, may be more disruptive for the corresponding mRNA secondary structures. This effect implies that synonymous mutations disrupting mRNA secondary structures may directly affect the fitness of the organism. These results demonstrate that the need to maintain intact mRNA structures imposes additional evolutionary constraints on bacterial genomes, which go beyond preservation of structure and function of the encoded proteins. PMID:23783573

A Catalog of Curriculum Materials for Marine Environment Studies--Elementary and Secondary.

ERIC Educational Resources Information Center

Delaware Univ., Newark. Coll. of Marine Studies.

This partially annotated bibliography on marine environment contains a list of learning experiences and curriculum units for elementary and secondary students. A majority of materials were published in the 1970s. Subjects include biological oceanography, which deals with general and specific aspects of marine biology such as plankton,…

Teachers as Secondary Players: Involvement in Field Trips to Natural Environments

ERIC Educational Resources Information Center

Alon, Nirit Lavie; Tal, Tali

2017-01-01

This study focused on field trips to natural environments where the teacher plays a secondary role alongside a professional guide. We investigated teachers' and field trip guides' views of the teacher's role, the teacher's actual function on the field trip, and the relationship between them. We observed field trips, interviewed teachers and…

Key Lessons for the Design and Integration of Virtual Environments in Secondary Science.

ERIC Educational Resources Information Center

Crosier, Joanna K.; Cobb, Sue; Wilson, John R.

2002-01-01

Discusses a three-year research project in which a virtual environment to teach radioactivity in secondary schools in the United Kingdom was developed and tested. Emphasizes the importance of involving teachers through the development process and confirms the importance of school-based evaluation studies in the development and evaluation of…

Unsecure School Environment and School Phobic Behavior

ERIC Educational Resources Information Center

Tukur, Abubakar Hamman; Muhammad, Khadijatu

2017-01-01

This study determines the level of student's school phobic behavior as a result of insecurity of school environment. The study was guided by one research question and one null hypothesis. The population of the study was all the secondary schools in Maiduguri, Borno state numbering about the same of the study was senior secondary students in…

Student Participation in Learning Environment Improvement: Analysis of a Co-Design Project in a Finnish Upper Secondary School

ERIC Educational Resources Information Center

Mäkelä, Tiina; Helfenstein, Sacha; Lerkkanen, Marja-Kristiina; Poikkeus, Anna-Maija

2018-01-01

The present educational design research involved analysing Finnish upper secondary school students' participation in the improvement of their psychosocial and technology-enhanced physical learning environment (LE). It examined which LE characteristics students considered important when redesigning their LE, and whether they felt that their ideas…

40 CFR 1037.620 - Shipment of incomplete vehicles to secondary vehicle manufacturers.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 34 2012-07-01 2012-07-01 false Shipment of incomplete vehicles to secondary vehicle manufacturers. 1037.620 Section 1037.620 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR POLLUTION CONTROLS CONTROL OF EMISSIONS FROM NEW HEAVY-DUTY MOTOR VEHICLES Special Compliance Provisions § 1037.620...

40 CFR 1037.620 - Shipment of incomplete vehicles to secondary vehicle manufacturers.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 34 2013-07-01 2013-07-01 false Shipment of incomplete vehicles to secondary vehicle manufacturers. 1037.620 Section 1037.620 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR POLLUTION CONTROLS CONTROL OF EMISSIONS FROM NEW HEAVY-DUTY MOTOR VEHICLES Special Compliance Provisions § 1037.620...

40 CFR 1037.620 - Shipment of incomplete vehicles to secondary vehicle manufacturers.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 33 2014-07-01 2014-07-01 false Shipment of incomplete vehicles to secondary vehicle manufacturers. 1037.620 Section 1037.620 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR POLLUTION CONTROLS CONTROL OF EMISSIONS FROM NEW HEAVY-DUTY MOTOR VEHICLES Special Compliance Provisions § 1037.620...

Predicting Girls' Learning Behaviour in Secondary School Mathematics Lessons from Motivational and Learning Environment Factors.

ERIC Educational Resources Information Center

Norwich, Brahm

1994-01-01

Reports on a study of 70 secondary female students in mathematics classes over a period of 7 weeks. Finds that self-efficacy was the best predictor of learning intentions. Recommends further research on the relationships between perceived learning environment, self-efficacy, and learning intentions. (CFR)

40 CFR 52.1875 - Attainment dates for achieving the sulfur dioxide secondary standard.

Code of Federal Regulations, 2013 CFR

2013-07-01

... sulfur dioxide secondary standard. 52.1875 Section 52.1875 Protection of Environment ENVIRONMENTAL... (CONTINUED) Ohio § 52.1875 Attainment dates for achieving the sulfur dioxide secondary standard. The attainment date for achieving the sulfur dioxide (SO2) secondary national ambient air quality standard (NAAQS...

40 CFR 52.1875 - Attainment dates for achieving the sulfur dioxide secondary standard.

Code of Federal Regulations, 2010 CFR

2010-07-01

... sulfur dioxide secondary standard. 52.1875 Section 52.1875 Protection of Environment ENVIRONMENTAL... (CONTINUED) Ohio § 52.1875 Attainment dates for achieving the sulfur dioxide secondary standard. The attainment date for achieving the sulfur dioxide (SO2) secondary national ambient air quality standard (NAAQS...

40 CFR 52.1875 - Attainment dates for achieving the sulfur dioxide secondary standard.

Code of Federal Regulations, 2011 CFR

2011-07-01

... sulfur dioxide secondary standard. 52.1875 Section 52.1875 Protection of Environment ENVIRONMENTAL... (CONTINUED) Ohio § 52.1875 Attainment dates for achieving the sulfur dioxide secondary standard. The attainment date for achieving the sulfur dioxide (SO2) secondary national ambient air quality standard (NAAQS...

40 CFR 52.1875 - Attainment dates for achieving the sulfur dioxide secondary standard.

Code of Federal Regulations, 2014 CFR

2014-07-01

... sulfur dioxide secondary standard. 52.1875 Section 52.1875 Protection of Environment ENVIRONMENTAL... (CONTINUED) Ohio § 52.1875 Attainment dates for achieving the sulfur dioxide secondary standard. The attainment date for achieving the sulfur dioxide (SO2) secondary national ambient air quality standard (NAAQS...

40 CFR 52.1875 - Attainment dates for achieving the sulfur dioxide secondary standard.

Code of Federal Regulations, 2012 CFR

2012-07-01

... sulfur dioxide secondary standard. 52.1875 Section 52.1875 Protection of Environment ENVIRONMENTAL... (CONTINUED) Ohio § 52.1875 Attainment dates for achieving the sulfur dioxide secondary standard. The attainment date for achieving the sulfur dioxide (SO2) secondary national ambient air quality standard (NAAQS...

On the Chemistry, Toxicology and Genetics of the Cyanobacterial Toxins, Microcystin, Nodularin, Saxitoxin and Cylindrospermopsin

PubMed Central

Pearson, Leanne; Mihali, Troco; Moffitt, Michelle; Kellmann, Ralf; Neilan, Brett

2010-01-01

The cyanobacteria or “blue-green algae”, as they are commonly termed, comprise a diverse group of oxygenic photosynthetic bacteria that inhabit a wide range of aquatic and terrestrial environments, and display incredible morphological diversity. Many aquatic, bloom-forming species of cyanobacteria are capable of producing biologically active secondary metabolites, which are highly toxic to humans and other animals. From a toxicological viewpoint, the cyanotoxins span four major classes: the neurotoxins, hepatotoxins, cytotoxins, and dermatoxins (irritant toxins). However, structurally they are quite diverse. Over the past decade, the biosynthesis pathways of the four major cyanotoxins: microcystin, nodularin, saxitoxin and cylindrospermopsin, have been genetically and biochemically elucidated. This review provides an overview of these biosynthesis pathways and additionally summarizes the chemistry and toxicology of these remarkable secondary metabolites. PMID:20559491

A generalized analysis of hydrophobic and loop clusters within globular protein sequences

PubMed Central

Eudes, Richard; Le Tuan, Khanh; Delettré, Jean; Mornon, Jean-Paul; Callebaut, Isabelle

2007-01-01

Background Hydrophobic Cluster Analysis (HCA) is an efficient way to compare highly divergent sequences through the implicit secondary structure information directly derived from hydrophobic clusters. However, its efficiency and application are currently limited by the need of user expertise. In order to help the analysis of HCA plots, we report here the structural preferences of hydrophobic cluster species, which are frequently encountered in globular domains of proteins. These species are characterized only by their hydrophobic/non-hydrophobic dichotomy. This analysis has been extended to loop-forming clusters, using an appropriate loop alphabet. Results The structural behavior of hydrophobic cluster species, which are typical of protein globular domains, was investigated within banks of experimental structures, considered at different levels of sequence redundancy. The 294 more frequent hydrophobic cluster species were analyzed with regard to their association with the different secondary structures (frequencies of association with secondary structures and secondary structure propensities). Hydrophobic cluster species are predominantly associated with regular secondary structures, and a large part (60 %) reveals preferences for α-helices or β-strands. Moreover, the analysis of the hydrophobic cluster amino acid composition generally allows for finer prediction of the regular secondary structure associated with the considered cluster within a cluster species. We also investigated the behavior of loop forming clusters, using a "PGDNS" alphabet. These loop clusters do not overlap with hydrophobic clusters and are highly associated with coils. Finally, the structural information contained in the hydrophobic structural words, as deduced from experimental structures, was compared to the PSI-PRED predictions, revealing that β-strands and especially α-helices are generally over-predicted within the limits of typical β and α hydrophobic clusters. Conclusion The dictionary of hydrophobic clusters described here can help the HCA user to interpret and compare the HCA plots of globular protein sequences, as well as provides an original fundamental insight into the structural bricks of protein folds. Moreover, the novel loop cluster analysis brings additional information for secondary structure prediction on the whole sequence through a generalized cluster analysis (GCA), and not only on regular secondary structures. Such information lays the foundations for developing a new and original tool for secondary structure prediction. PMID:17210072

Flow structures and sandbar dynamics in a canyon river during a controlled flood, Colorado River, Arizona

USGS Publications Warehouse

Wright, S.A.; Kaplinski, M.

2011-01-01

In canyon rivers, debris fan constrictions create rapids and downstream pools characterized by secondary flow structures that are closely linked to channel morphology. In this paper we describe detailed measurements of the three-dimensional flow structure and sandbar dynamics of two pools along the Colorado River in the Grand Canyon during a controlled flood release from Glen Canyon Dam. Results indicate that the pools are characterized by large lateral recirculation zones (eddies) resulting from flow separation downstream from the channel constrictions, as well as helical flow structures in the main channel and eddy. The lateral recirculation zones are low-velocity areas conducive to fine sediment deposition, particularly in the vicinity of the separation and reattachment points and are thus the dominant flow structures controlling sandbar dynamics. The helical flow structures also affect morphology but appear secondary in importance to the lateral eddies. During the controlled flood, sandbars in the separation and reattachment zones at both sites tended to build gradually during the rising limb and peak flow. Deposition in shallow water on the sandbars was accompanied by erosion in deeper water along the sandbar slope at the interface with the main channel. Erosion occurred via rapid mass failures as well as by gradual boundary shear stress driven processes. The flow structures and morphologic links at our study sites are similar to those identified in other river environments, in particular sharply curved meanders and channel confluences where the coexistence of lateral recirculation and helical flows has been documented. Copyright 2011 by the American Geophysical Union.

Impacts of structuring the electronic health record: Results of a systematic literature review from the perspective of secondary use of patient data.

PubMed

Vuokko, Riikka; Mäkelä-Bengs, Päivi; Hyppönen, Hannele; Lindqvist, Minna; Doupi, Persephone

2017-01-01

To explore the impacts that structuring of electronic health records (EHRs) has had from the perspective of secondary use of patient data as reflected in currently published literature. This paper presents the results of a systematic literature review aimed at answering the following questions; (1) what are the common methods of structuring patient data to serve secondary use purposes; (2) what are the common methods of evaluating patient data structuring in the secondary use context, and (3) what impacts or outcomes of EHR structuring have been reported from the secondary use perspective. The reported study forms part of a wider systematic literature review on the impacts of EHR structuring methods and evaluations of their impact. The review was based on a 12-step systematic review protocol adapted from the Cochrane methodology. Original articles included in the study were divided into three groups for analysis and reporting based on their use focus: nursing documentation, medical use and secondary use (presented in this paper). The analysis from the perspective of secondary use of data includes 85 original articles from 1975 to 2010 retrieved from 15 bibliographic databases. The implementation of structured EHRs can be roughly divided into applications for documenting patient data at the point of care and application for retrieval of patient data (post hoc structuring). Two thirds of the secondary use articles concern EHR structuring methods which were still under development or in the testing phase. of structuring patient data such as codes, terminologies, reference information models, forms or templates and documentation standards were usually applied in combination. Most of the identified benefits of utilizing structured EHR data for secondary use purposes concentrated on information content and quality or on technical quality and reliability, particularly in the case of Natural Language Processing (NLP) studies. A few individual articles evaluated impacts on care processes, productivity and costs, patient safety, care quality or other health impacts. In most articles these endpoints were usually discussed as goals of secondary use and less as evidence-supported impacts, resulting from the use of structured EHR data for secondary purposes. Further studies and more sound evaluation methods are needed for evidence on how EHRs are utilized for secondary purposes, and how structured documentation methods can serve different users' needs, e.g. administration, statistics and research and development, in parallel to medical use purposes. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Optimising measurement of health-related characteristics of the built environment: Comparing data collected by foot-based street audits, virtual street audits and routine secondary data sources.

PubMed

Pliakas, Triantafyllos; Hawkesworth, Sophie; Silverwood, Richard J; Nanchahal, Kiran; Grundy, Chris; Armstrong, Ben; Casas, Juan Pablo; Morris, Richard W; Wilkinson, Paul; Lock, Karen

2017-01-01

The role of the neighbourhood environment in influencing health behaviours continues to be an important topic in public health research and policy. Foot-based street audits, virtual street audits and secondary data sources are widespread data collection methods used to objectively measure the built environment in environment-health association studies. We compared these three methods using data collected in a nationally representative epidemiological study in 17 British towns to inform future development of research tools. There was good agreement between foot-based and virtual audit tools. Foot based audits were superior for fine detail features. Secondary data sources measured very different aspects of the local environment that could be used to derive a range of environmental measures if validated properly. Future built environment research should design studies a priori using multiple approaches and varied data sources in order to best capture features that operate on different health behaviours at varying spatial scales. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Potential Cement Phases in Sedimentary Rocks Drilled by Curiosity at Gale Crater, Mars

NASA Technical Reports Server (NTRS)

Rampe, E. B.; Morris, R. V.; Bish, D. L.; Chipera, S. J.; Ming, D. W.; Blake, D. F.; Vaniman, D. T.; Bristow, T. F.; Cavanagh, P.; Farmer, J. D.;

Validity of secondary retail food outlet data: a systematic review.

PubMed

Fleischhacker, Sheila E; Evenson, Kelly R; Sharkey, Joseph; Pitts, Stephanie B Jilcott; Rodriguez, Daniel A

2013-10-01

Improving access to healthy foods is a promising strategy to prevent nutrition-related chronic diseases. To characterize retail food environments and identify areas with limited retail access, researchers, government programs, and community advocates have primarily used secondary retail food outlet data sources (e.g., InfoUSA or government food registries). To advance the state of the science on measuring retail food environments, this systematic review examined the evidence for validity reported for secondary retail food outlet data sources for characterizing retail food environments. A literature search was conducted through December 31, 2012, to identify peer-reviewed published literature that compared secondary retail food outlet data sources to primary data sources (i.e., field observations) for accuracy of identifying the type and location of retail food outlets. Data were analyzed in 2013. Nineteen studies met the inclusion criteria. The evidence for validity reported varied by secondary data sources examined, primary data-gathering approaches, retail food outlets examined, and geographic and sociodemographic characteristics. More than half of the studies (53%) did not report evidence for validity by type of food outlet examined and by a particular secondary data source. Researchers should strive to gather primary data but if relying on secondary data sources, InfoUSA and government food registries had higher levels of agreement than reported by other secondary data sources and may provide sufficient accuracy for exploring these associations in large study areas. Published by Elsevier Inc. on behalf of American Journal of Preventive Medicine.

Nursing Clinical Instructor Experiences of Empowerment in Rwanda: Applying Kanter's and Spreitzer's Theories.

PubMed

Thuss, Mary; Babenko-Mould, Yolanda; Andrusyszyn, Mary-Anne; Laschinger, Heather K S

2016-10-15

The purpose of this study was to explore Rwandan nursing clinical instructors' (CIs) experiences of structural and psychological empowerment. CIs play a vital role in students' development by facilitating learning in health care practice environments. Quality nursing education hinges on the CI's ability to enact a professional role. A descriptive qualitative method was used to obtain an understanding of CIs empowerment experiences in practice settings. Kanter's Theory of Structural Power in Organizations and Spreitzer's Psychological Empowerment Theory were used as theoretical frameworks to interpret experiences. Interview data from 21 CIs were used to complete a secondary analysis. Most participants perceived the structural components of informal power, resources, and support while formal power and opportunity were limited, diminishing their sense of structural empowerment. Psychological empowerment for CIs stemmed from a sense of competence, meaning, impact and self-determination they had for their teaching roles and responsibilities in the practice setting.

Structural stability of myoglobin and glycomyoglobin: a comparative molecular dynamics simulation study.

PubMed

Alizadeh-Rahrovi, Joulia; Shayesteh, Alireza; Ebrahim-Habibi, Azadeh

2015-09-01

Glycoproteins are formed as the result of enzymatic glycosylation or chemical glycation in the body, and produced in vitro in industrial processes. The covalently attached carbohydrate molecule(s) confer new properties to the protein, including modified stability. In the present study, the structural stability of a glycoprotein form of myoglobin, bearing a glucose unit in the N-terminus, has been compared with its native form by the use of molecular dynamics simulation. Both structures were subjected to temperatures of 300 and 500 K in an aqueous environment for 10 ns. Changes in secondary structures and RMSD were then assessed. An overall higher stability was detected for glycomyoglobin, for which the most stable segments/residues were highlighted and compared with the native form. The simple addition of a covalently bound glucose is suggested to exert its stabilizing effect via increased contacts with surrounding water molecules, as well as a different pattern of interactions with neighbor residues.

An experimental study of secondary vortex structure in mixing layers

NASA Technical Reports Server (NTRS)

Bell, J. H.; Mehta, Rabindra D.

1990-01-01

This report covers the first eight months of an experimental research project on the secondary vortex structure in plane mixing layers. The aim of the project is to obtain quantitative data on the behavior of the secondary structure in a turbulent mixing layer at reasonable reynolds numbers (Re(sub delta(sub w)) approx. 50,000). In particular, we hope to resolve the questions of how the scale of the secondary vortex structure changes with the scale of the mixing layer, and whether the structures are fixed in space, or whether they 'meander' in the spanwise direction.

Convergence of an iterative procedure for large-scale static analysis of structural components

NASA Technical Reports Server (NTRS)

Austin, F.; Ojalvo, I. U.

1976-01-01

The paper proves convergence of an iterative procedure for calculating the deflections of built-up component structures which can be represented as consisting of a dominant, relatively stiff primary structure and a less stiff secondary structure, which may be composed of one or more substructures that are not connected to one another but are all connected to the primary structure. The iteration consists in estimating the deformation of the primary structure in the absence of the secondary structure on the assumption that all mechanical loads are applied directly to the primary structure. The j-th iterate primary structure deflections at the interface are imposed on the secondary structure, and the boundary loads required to produce these deflections are computed. The cycle is completed by applying the interface reaction to the primary structure and computing its updated deflections. It is shown that the mathematical condition for convergence of this procedure is that the maximum eigenvalue of the equation relating primary-structure deflection to imposed secondary-structure deflection be less than unity, which is shown to correspond with the physical requirement that the secondary structure be more flexible at the interface boundary.

A Selected Bibliography on the Relevance of Environmental Education to Secondary School Curricula.

ERIC Educational Resources Information Center

Cunningham, Michael C., Comp.; Cunningham, Cheryl Bond, Comp.

The intent of this bibliography is to provide resources for the secondary school teacher concerning (1) substantive information about the environment and (2) means and methods of communicating that information in the classroom. It deals primarily with the man-made environment rather than with environmental resources and has an urban bias - not one…

The Intersection of Mathematics and Language in the Post-Secondary Environment: Implications for English Language Learners

ERIC Educational Resources Information Center

Choi, Jean; Milburn, Rebecca; Reynolds, Brett; Marcoccia, Philip; Silva, Patrick Justin; Panag, Sikander

2013-01-01

Given the increasing number of English Language Learners (ELLs) in post-secondary environments (Roessingh & Douglas, 2012), educational practices such as availability of language support for mathematics should be assessed to ensure that all students' needs are met. To explore the effects of language on mathematics in ELLs, mathematical test…

Using Videoconferencing to Provide Mentorship in Inquiry-Based Urban and Rural Secondary Classrooms

ERIC Educational Resources Information Center

Li, Qing; Dyjur, Patricia; Nicholson, Natalya; Moorman, Lynn

2009-01-01

The main purpose of this design-based research study is to examine the effects of an inquiry-based learning environment, with the support of videoconferencing, on both rural and urban secondary students' mathematics and science learning. An important aspect of this learning environment is the use of videoconferencing to connect classes with…

Queering the Environment and Caring for the Self: Icelandic LGBT Students' Experience of the Upper Secondary School

ERIC Educational Resources Information Center

Kjaran, Jón; Kristinsdóttir, Guðrún

2015-01-01

Heteronormative culture and heterosexism is experienced by many LGBT students and queer individuals in their daily interactions with their environment. Icelandic upper secondary schools are no exception in this respect. This article draws on interview data with five LGBT students supported by semi-participatory observations at two upper secondary…

My Pocket Technology: Introducing a Mobile Assisted Inquiry Learning Environment (MAILE) to Promote Inquiries among Secondary Students

ERIC Educational Resources Information Center

Leelamma, Sreelekha; Indira, Uma Devi

2017-01-01

This paper introduces the Mobile Assisted Inquiry Learning Environment (MAILE), an Experimental Instructional Strategy (EIS) which employs an inquiry-based learning approach to guide secondary school students to learn environmental science in an engaging way supported by mobile phones. The students are situated in both the real world and the…

Finnish Upper Secondary Students' Collaborative Processes in Learning Statistics in a CSCL Environment

ERIC Educational Resources Information Center

Oikarinen, Juho Kaleva; Järvelä, Sanna; Kaasila, Raimo

2014-01-01

This design-based research project focuses on documenting statistical learning among 16-17-year-old Finnish upper secondary school students (N = 78) in a computer-supported collaborative learning (CSCL) environment. One novel value of this study is in reporting the shift from teacher-led mathematical teaching to autonomous small-group learning in…

Personal goals as predictors of intended classroom goals: comparing elementary and secondary school pre-service teachers.

PubMed

Daniels, Lia M; Frenzel, Anne C; Stupnisky, Robert H; Stewart, Tara L; Perry, Raymond P

2013-09-01

The literature documents fewer classroom mastery goal structures in secondary school compared to elementary. However, little is known about how personal achievement goals may influence classroom goal structures. This is especially true at the level of pre-service teachers. Our objective was to investigate if pre-service teachers' personal goals predicted their intended classroom goal structures. Participants were 125 elementary and 175 secondary school pre-service teachers from two Western Canadian universities. Structural equation modelling was used to examine if the structural relationships and latent means of personal and intended classroom goal structures differed for elementary and secondary school pre-service teachers. The results revealed that personal goals predicted the goal structures that pre-service teachers intended to establish; however, the relationships and means differed between elementary and secondary school pre-service teachers. Specifically, personal mastery-approach goals positively predicted classroom mastery goals much more strongly at the elementary than the secondary level. Furthermore, elementary pre-service teachers had significantly higher latent mean scores on personal mastery-approach goals than their secondary counterparts. It seems possible that the currently documented differences between classroom goal structures noted for elementary compared to secondary school may be based on the personal goals endorsed as pre-service teachers. The results are further discussed in terms of alignment with research on practising teachers' personal and classroom goals and implications for teacher education. © 2012 The British Psychological Society.

40 CFR 50.16 - National primary and secondary ambient air quality standards for lead.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 2 2010-07-01 2010-07-01 false National primary and secondary ambient... AGENCY (CONTINUED) AIR PROGRAMS NATIONAL PRIMARY AND SECONDARY AMBIENT AIR QUALITY STANDARDS § 50.16 National primary and secondary ambient air quality standards for lead. (a) The national primary and...

40 CFR 421.180 - Applicability: Description of the primary and secondary germanium and gallium subcategory.

Code of Federal Regulations, 2010 CFR

2010-07-01

... primary and secondary germanium and gallium subcategory. 421.180 Section 421.180 Protection of Environment... POINT SOURCE CATEGORY Primary and Secondary Germanium and Gallium Subcategory § 421.180 Applicability: Description of the primary and secondary germanium and gallium subcategory. The provisions of this subpart are...

40 CFR 421.180 - Applicability: Description of the primary and secondary germanium and gallium subcategory.

Code of Federal Regulations, 2011 CFR

2011-07-01

... primary and secondary germanium and gallium subcategory. 421.180 Section 421.180 Protection of Environment... POINT SOURCE CATEGORY Primary and Secondary Germanium and Gallium Subcategory § 421.180 Applicability: Description of the primary and secondary germanium and gallium subcategory. The provisions of this subpart are...

40 CFR 421.180 - Applicability: Description of the primary and secondary germanium and gallium subcategory.

Code of Federal Regulations, 2014 CFR

2014-07-01

... primary and secondary germanium and gallium subcategory. 421.180 Section 421.180 Protection of Environment... POINT SOURCE CATEGORY Primary and Secondary Germanium and Gallium Subcategory § 421.180 Applicability: Description of the primary and secondary germanium and gallium subcategory. The provisions of this subpart are...

40 CFR 421.180 - Applicability: Description of the primary and secondary germanium and gallium subcategory.

Code of Federal Regulations, 2012 CFR

2012-07-01

... primary and secondary germanium and gallium subcategory. 421.180 Section 421.180 Protection of Environment... POINT SOURCE CATEGORY Primary and Secondary Germanium and Gallium Subcategory § 421.180 Applicability: Description of the primary and secondary germanium and gallium subcategory. The provisions of this subpart are...

40 CFR 421.180 - Applicability: Description of the primary and secondary germanium and gallium subcategory.

Code of Federal Regulations, 2013 CFR

2013-07-01

... primary and secondary germanium and gallium subcategory. 421.180 Section 421.180 Protection of Environment... POINT SOURCE CATEGORY Primary and Secondary Germanium and Gallium Subcategory § 421.180 Applicability: Description of the primary and secondary germanium and gallium subcategory. The provisions of this subpart are...

40 CFR 721.10007 - Alcohols, C12-14-secondary, ethoxylated propoxylated.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Alcohols, C12-14-secondary... New Uses for Specific Chemical Substances § 721.10007 Alcohols, C12-14-secondary, ethoxylated... identified as alcohols, C12-14- secondary, ethoxylated propoxylated (PMN P-00-11; CAS No. 103331-86-8) is...

40 CFR 721.9220 - Reaction products of secondary alkyl amines with a substituted benzenesulfonic acid and sulfuric...

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Reaction products of secondary alkyl... Reaction products of secondary alkyl amines with a substituted benzenesulfonic acid and sulfuric acid... substances identified generically as reaction products of secondary alkyl amines with a substituted...

40 CFR 721.9220 - Reaction products of secondary alkyl amines with a substituted benzenesulfonic acid and sulfuric...

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Reaction products of secondary alkyl... Reaction products of secondary alkyl amines with a substituted benzenesulfonic acid and sulfuric acid... substances identified generically as reaction products of secondary alkyl amines with a substituted...

Metastable ripple phase of fully hydrated dipalmitoylphosphatidylcholine as studied by small angle x-ray scattering

PubMed Central

Yao, Haruhiko; Matuoka, Sinzi; Tenchov, Boris; Hatta, Ichiro

1991-01-01

Fully hydrated dipalmitoylphosphatidylcholine (DPPC) undergoes liquid crystalline to metastable Pβ, phase transition in cooling. A small angle x-ray scattering study has been performed for obtaining further evidence about the structure of this phase. From a high-resolution observation of x-ray diffraction profiles, a distinct multipeak pattern has become obvious. Among them the (01) reflection in the secondary ripple structure is identified clearly. There are peaks assigned straightforwardly to (10) and (20) reflections in the primary ripple structure and peaks assigned to (10) and (20) reflections in the secondary ripple structure. Therefore the multipeak pattern is due to superposition of the reflections cause by the primary and secondary ripple structures. The lattice parameters are estimated as follows: for the primary ripple structure a = 7.09 nm, b = 13.64 nm, and γ = 95°, and for the secondary ripple structure a = 8.2 nm, b = 26.6 nm, and γ = 90°. The lattice parameters thus obtained for the secondary ripple structure are not conclusive, however. The hydrocarbon chains in the primary ripple structure have been reported as being tilted against the bilayer plane and, on the other hand, the hydrocarbon chains in the secondary ripple structure are likely to be perpendicular to the bilayer plane. This fact seems to be related to a sequential mechanism of phase transitions. On heating from the Lβ, phase where the hydrocarbon chains are tilted the primary ripple structure having tilted hydrocarbon chains takes place and on cooling from the Lα phase where the hydrocarbon chains are not tilted the secondary ripple structure with untilted chains tends to be stabilized. It appears that the truly metastable ripple phase is expressed by the second ripple structure although in the course of the actual cooling transition both the secondary and primary ripple structures form and coexist. PMID:19431787

Structural characterization of proteins in wheat flour doughs enriched with intermediate wheatgrass (Thinopyrum intermedium) flour.

PubMed

Marti, Alessandra; Bock, Jayne E; Pagani, Maria Ambrogina; Ismail, Baraem; Seetharaman, Koushik

2016-03-01

The high protein and fiber content of intermediate wheatgrass (IWG) - together with its interesting agronomic traits and environment-related benefits - make this perennial crop attractive also for human consumption. Structural characteristics of the proteins in IWG/hard wheat flour (HWF) doughs (at IWG:HWF ratios of 0:100, 50:50, 75:25 and 100:0) - including aggregate formation, thiols availability, and secondary structure changes during dough mixing - were investigated. Proteins in IWG-doughs had higher solubility and thiol content - as function of IWG content - suggesting that protein network was mostly based on non-covalent interactions. While 50% IWG-enrichment gave an increase in random structures, enrichment at ⩾75% resulted in a decrease in β-sheets with an increase in random structures, indicating a decrease in structural order. The observed differences in protein molecular configuration and interactions in HWF compared to IWG doughs necessitate further investigation to establish their impact on the quality of IWG-enriched bread. Copyright © 2015 Elsevier Ltd. All rights reserved.

Stem-Loop RNA Hairpins in Giant Viruses: Invading rRNA-Like Repeats and a Template Free RNA

PubMed Central

Seligmann, Hervé; Raoult, Didier

2018-01-01

We examine the hypothesis that de novo template-free RNAs still form spontaneously, as they did at the origins of life, invade modern genomes, contribute new genetic material. Previously, analyses of RNA secondary structures suggested that some RNAs resembling ancestral (t)RNAs formed recently de novo, other parasitic sequences cluster with rRNAs. Here positive control analyses of additional RNA secondary structures confirm ancestral and de novo statuses of RNA grouped according to secondary structure. Viroids with branched stems resemble de novo RNAs, rod-shaped viroids resemble rRNA secondary structures, independently of GC contents. 5′ UTR leading regions of West Nile and Dengue flavivirid viruses resemble de novo and rRNA structures, respectively. An RNA homologous with Megavirus, Dengue and West Nile genomes, copperhead snake microsatellites and levant cotton repeats, not templated by Mimivirus' genome, persists throughout Mimivirus' infection. Its secondary structure clusters with candidate de novo RNAs. The saltatory phyletic distribution and secondary structure of Mimivirus' peculiar RNA suggest occasional template-free polymerization of this sequence, rather than noncanonical transcriptions (swinger polymerization, posttranscriptional editing). PMID:29449833

On the Sequence-Directed Nature of Human Gene Mutation: The Role of Genomic Architecture and the Local DNA Sequence Environment in Mediating Gene Mutations Underlying Human Inherited Disease

PubMed Central

Cooper, David N.; Bacolla, Albino; Férec, Claude; Vasquez, Karen M.; Kehrer-Sawatzki, Hildegard; Chen, Jian-Min

2011-01-01

Different types of human gene mutation may vary in size, from structural variants (SVs) to single base-pair substitutions, but what they all have in common is that their nature, size and location are often determined either by specific characteristics of the local DNA sequence environment or by higher-order features of the genomic architecture. The human genome is now recognized to contain ‘pervasive architectural flaws’ in that certain DNA sequences are inherently mutation-prone by virtue of their base composition, sequence repetitivity and/or epigenetic modification. Here we explore how the nature, location and frequency of different types of mutation causing inherited disease are shaped in large part, and often in remarkably predictable ways, by the local DNA sequence environment. The mutability of a given gene or genomic region may also be influenced indirectly by a variety of non-canonical (non-B) secondary structures whose formation is facilitated by the underlying DNA sequence. Since these non-B DNA structures can interfere with subsequent DNA replication and repair, and may serve to increase mutation frequencies in generalized fashion (i.e. both in the context of subtle mutations and SVs), they have the potential to serve as a unifying concept in studies of mutational mechanisms underlying human inherited disease. PMID:21853507

Predicting healthy and unhealthy behaviors through physical education: A self-determination theory-based longitudinal approach.

PubMed

Ferriz, R; González-Cutre, D; Sicilia, Á; Hagger, M S

2016-05-01

The aim of this study was to evaluate the relations between three dimensions of the structured teaching environment (promotion of theoretical knowledge, physical learning, and health improvement) in physical education (PE) and the adoption of health-related behaviors by students. The study adopted a two-occasion longitudinal design based on self-determination theory (SDT). PE students (N = 654, mean age = 16.13, SD = .77) completed measures of perceived structured teaching environment, satisfaction of basic psychological needs and motivation for PE, and healthy (physical activity, sport participation, and healthy eating) and unhealthy (consumption of tobacco, alcohol, and drugs) behaviors at the beginning and end of the first year of post-compulsory secondary education. Path analysis of the proposed relations among variables supported SDT tenets and showed positive relations between the three dimensions of the structured teaching environment, the satisfaction of basic psychological needs, and autonomous motivation in PE. Autonomous motivation contributed to an explanation of variance in two healthy behaviors, physical activity and sport participation. However, no relation was found among motivation in PE, healthy eating, and consumption of tobacco, alcohol, and drugs. These results show negligible trans-contextual influence of SDT motivational factors in PE on other healthy behaviors beyond physical activity. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Correlates of school dropout and absenteeism among adolescent girls from marginalized community in north Karnataka, south India.

PubMed

Prakash, Ravi; Beattie, Tara; Javalkar, Prakash; Bhattacharjee, Parinita; Ramanaik, Satyanarayana; Thalinja, Raghavendra; Murthy, Srikanta; Davey, Calum; Blanchard, James; Watts, Charlotte; Collumbien, Martine; Moses, Stephen; Heise, Lori; Isac, Shajy

2017-12-01

Secondary education among lower caste adolescent girls living in rural Karnataka, South India, is characterized by high rates of school drop-out and absenteeism. A cross-sectional baseline survey (N=2275) was conducted in 2014 as part of a cluster-randomized control trial among adolescent girls (13-14 year) and their families from marginalized communities in two districts of north Karnataka. Bivariate and multivariate logistic regression models were used. Overall, 8.7% girls reported secondary school dropout and 8.1% reported frequent absenteeism (past month). In adjusted analyses, economic factors (household poverty; girls' work-related migration), social norms and practices (child marriage; value of girls' education), and school-related factors (poor learning environment and bullying/harassment at school) were associated with an increased odds of school dropout and absenteeism. Interventions aiming to increase secondary school retention among marginalized girls may require a multi-level approach, with synergistic components that address social, structural and economic determinants of school absenteeism and dropout. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

A marine secondary producer respires and feeds more in a high CO2 ocean.

PubMed

Li, Wei; Gao, Kunshan

2012-04-01

Climate change mediates marine chemical and physical environments and therefore influences marine organisms. While increasing atmospheric CO(2) level and associated ocean acidification has been predicted to stimulate marine primary productivity and may affect community structure, the processes that impact food chain and biological CO(2) pump are less documented. We hypothesized that copepods, as the secondary marine producer, may respond to future changes in seawater carbonate chemistry associated with ocean acidification due to increasing atmospheric CO(2) concentration. Here, we show that the copepod, Centropages tenuiremis, was able to perceive the chemical changes in seawater induced under elevated CO(2) concentration (>1700 μatm, pH<7.60) with avoidance strategy. The copepod's respiration increased at the elevated CO(2) (1000 μatm), associated acidity (pH 7.83) and its feeding rates also increased correspondingly, except for the initial acclimating period, when it fed less. Our results imply that marine secondary producers increase their respiration and feeding rate in response to ocean acidification to balance the energy cost against increased acidity and CO(2) concentration. Copyright © 2012 Elsevier Ltd. All rights reserved.

RNAstructure: software for RNA secondary structure prediction and analysis.

PubMed

Reuter, Jessica S; Mathews, David H

2010-03-15

To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence. RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. The original graphical user interface for Microsoft Windows is still maintained. The extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package is available for download from the Mathews lab homepage at http://rna.urmc.rochester.edu/RNAstructure.html.

Study on the Effect of Secondary Banded Structure on the Fatigue Property of Non-Quenched and Tempered Micro Alloyed Steel

NASA Astrophysics Data System (ADS)

Yajie, Cheng; Qingliang, Liao; Yue, Zhang

Due to composition segregation and cooling speed, streamline or banded structure were often obtained in the thermal forming parts along the direction of parts forming. Generally speaking, banded structure doesn't decrease the longitudinal mechanical properties, so the secondary banded structure can't get enough attention. The effect of secondary banded structure on the fatigue properties of micro alloyed DG20Mn and 35CrMo steel was investigated using the axial tensile fatigue test of stress ratio of 0.1. The result shows that secondary banded structure was obtained in the center of the steel parts, because of the composition segregation and the lower cooling rate in center part of steel. Secondary banded structure has no significant effect on axial tensile properties of both DG20Mn and 35CrMo, but decreases the axial tensile fatigue performance of DG20Mn steel. This study suggests that under the high cyclic tensile stress, multi-source damage cracks in steel initiated by large strain of pearlite of secondary banded structure, which is larger than damage strain, is the major factor of the decrease of fatigue life of steel.

DNA Secondary Structure at Chromosomal Fragile Sites in Human Disease

PubMed Central

Thys, Ryan G; Lehman, Christine E; Pierce, Levi C. T; Wang, Yuh-Hwa

2015-01-01

DNA has the ability to form a variety of secondary structures that can interfere with normal cellular processes, and many of these structures have been associated with neurological diseases and cancer. Secondary structure-forming sequences are often found at chromosomal fragile sites, which are hotspots for sister chromatid exchange, chromosomal translocations, and deletions. Structures formed at fragile sites can lead to instability by disrupting normal cellular processes such as DNA replication and transcription. The instability caused by disruption of replication and transcription can lead to DNA breakage, resulting in gene rearrangements and deletions that cause disease. In this review, we discuss the role of DNA secondary structure at fragile sites in human disease. PMID:25937814

Dimensionality and construct validity of an instrument designed to measure the metacognitive orientation of science classroom learning environments.

PubMed

Thomas, Gregory P

2004-01-01

The purpose of this study was to establish the factorial construct validity and dimensionality of the Metacognitive Orientation Learning Environment Scale-Science (MOLES-S) which was designed to measure the metacognitive orientation of science classroom learning environments. The metacognitive orientation of a science classroom learning environment is the extent to which psychosocial conditions that are known to enhance students' metacognition are evident within that classroom. The development of items comprising this scale was based on a theoretical understanding of metacognition, learning environments and the development of previous learning environments instruments. Four possible hypothesized structure models, each consistent with the literature, were reviewed and their merits were compared on the basis of empirical data drawn from two populations of 1026 and 1223 Hong Kong secondary school students using confirmatory factor analysis procedures. The scale was calibrated using the Rasch rating scale model using data from the 1223 student sample. The results suggest that there is strong evidence to support the factorial construct validity of the MOLES-S but that, on the basis of the Rasch analysis, there are still suggestions for further refinement and improvement of the MOLES-S.

Protein secondary structure prediction using modular reciprocal bidirectional recurrent neural networks.

PubMed

Babaei, Sepideh; Geranmayeh, Amir; Seyyedsalehi, Seyyed Ali

2010-12-01

The supervised learning of recurrent neural networks well-suited for prediction of protein secondary structures from the underlying amino acids sequence is studied. Modular reciprocal recurrent neural networks (MRR-NN) are proposed to model the strong correlations between adjacent secondary structure elements. Besides, a multilayer bidirectional recurrent neural network (MBR-NN) is introduced to capture the long-range intramolecular interactions between amino acids in formation of the secondary structure. The final modular prediction system is devised based on the interactive integration of the MRR-NN and the MBR-NN structures to arbitrarily engage the neighboring effects of the secondary structure types concurrent with memorizing the sequential dependencies of amino acids along the protein chain. The advanced combined network augments the percentage accuracy (Q₃) to 79.36% and boosts the segment overlap (SOV) up to 70.09% when tested on the PSIPRED dataset in three-fold cross-validation. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

New insights from cluster analysis methods for RNA secondary structure prediction

PubMed Central

Rogers, Emily; Heitsch, Christine

2016-01-01

A widening gap exists between the best practices for RNA secondary structure prediction developed by computational researchers and the methods used in practice by experimentalists. Minimum free energy (MFE) predictions, although broadly used, are outperformed by methods which sample from the Boltzmann distribution and data mine the results. In particular, moving beyond the single structure prediction paradigm yields substantial gains in accuracy. Furthermore, the largest improvements in accuracy and precision come from viewing secondary structures not at the base pair level but at lower granularity/higher abstraction. This suggests that random errors affecting precision and systematic ones affecting accuracy are both reduced by this “fuzzier” view of secondary structures. Thus experimentalists who are willing to adopt a more rigorous, multilayered approach to secondary structure prediction by iterating through these levels of granularity will be much better able to capture fundamental aspects of RNA base pairing. PMID:26971529

Assessment of the Influence of the RaD-X Balloon Payload on the Onboard Radiation Detectors

NASA Technical Reports Server (NTRS)

Gronoff, Guilluame; Mertens, Christopher J.; Norman, Ryan B.; Straume, Tore; Lusby, Terry C.

2016-01-01

The NASA Radiation Dosimetry Experiment (RaD-X) stratospheric balloon flight mission, launched on 25 September 2015, provided dosimetric measurements above the Pfotzer maximum. The goal of taking these measurements is to improve aviation radiation models by providing a characterization of cosmic ray primaries, which are the source of radiation exposure at aviation altitudes. The RaD-X science payload consists of four instruments. The main science instrument is a tissue-equivalent proportional counter (TEPC). The other instruments consisted of three solid state silicon dosimeters: Liulin, Teledyne total ionizing dose (TID) and RaySure detectors. The instruments were housed in an aluminum structure protected by a foam cover. The structure partially shielded the detectors from cosmic rays but also created secondary particles, modifying the ambient radiation environment observed by the instruments. Therefore, it is necessary to account for the influence of the payload structure on the measured doses. In this paper, we present the results of modeling the effect of the balloon payload on the radiation detector measurements using a Geant-4 (GEometry ANd Tracking) application. Payload structure correction factors derived for the TEPC, Liulin, and TID instruments are provided as a function of altitude. Overall, the payload corrections are no more than a 7% effect on the radiation environment measurements.

Canopy Temperature and Vegetation Indices from High-Throughput Phenotyping Improve Accuracy of Pedigree and Genomic Selection for Grain Yield in Wheat

PubMed Central

Rutkoski, Jessica; Poland, Jesse; Mondal, Suchismita; Autrique, Enrique; Pérez, Lorena González; Crossa, José; Reynolds, Matthew; Singh, Ravi

2016-01-01

Genomic selection can be applied prior to phenotyping, enabling shorter breeding cycles and greater rates of genetic gain relative to phenotypic selection. Traits measured using high-throughput phenotyping based on proximal or remote sensing could be useful for improving pedigree and genomic prediction model accuracies for traits not yet possible to phenotype directly. We tested if using aerial measurements of canopy temperature, and green and red normalized difference vegetation index as secondary traits in pedigree and genomic best linear unbiased prediction models could increase accuracy for grain yield in wheat, Triticum aestivum L., using 557 lines in five environments. Secondary traits on training and test sets, and grain yield on the training set were modeled as multivariate, and compared to univariate models with grain yield on the training set only. Cross validation accuracies were estimated within and across-environment, with and without replication, and with and without correcting for days to heading. We observed that, within environment, with unreplicated secondary trait data, and without correcting for days to heading, secondary traits increased accuracies for grain yield by 56% in pedigree, and 70% in genomic prediction models, on average. Secondary traits increased accuracy slightly more when replicated, and considerably less when models corrected for days to heading. In across-environment prediction, trends were similar but less consistent. These results show that secondary traits measured in high-throughput could be used in pedigree and genomic prediction to improve accuracy. This approach could improve selection in wheat during early stages if validated in early-generation breeding plots. PMID:27402362

Student-Centred and Teacher-Centred Learning Environment in Pre-Vocational Secondary Education: Psychological Needs, and Motivation

ERIC Educational Resources Information Center

Smit, Karin; de Brabander, Cornelis J.; Martens, Rob L.

2014-01-01

In this study the perception of psychological needs and motivation in a student-centred and a teacher-centred learning environment are compared, using Self Determination Theory as a framework. The self-report Intrinsic Motivation Inventory was completed by 230 students (mean age 16.1 years) in pre-vocational secondary education. School records on…

Diagnosing Learners' Problem-Solving Strategies Using Learning Environments with Algorithmic Problems in Secondary Education

ERIC Educational Resources Information Center

Kiesmuller, Ulrich

2009-01-01

At schools special learning and programming environments are often used in the field of algorithms. Particularly with regard to computer science lessons in secondary education, they are supposed to help novices to learn the basics of programming. In several parts of Germany (e.g., Bavaria) these fundamentals are taught as early as in the seventh…

Examining the Attitudes of Secondary General Education and Special Education Teachers toward Inclusion of Children with Autism in General Education Classrooms

ERIC Educational Resources Information Center

Bosch, Morghan E.

2016-01-01

Academic environments, such as general education classrooms, have increasingly become important learning environments for children with autism. The purpose of the study was to examine the attitudes of secondary general education and special education teachers toward inclusion of children with autism in general education classrooms. The research…

Are Environmental Influences on Physical Activity Distinct for Urban, Suburban, and Rural Schools? A Multilevel Study among Secondary School Students in Ontario, Canada

ERIC Educational Resources Information Center

Hobin, Erin P.; Leatherdale, Scott; Manske, Steve; Dubin, Joel A.; Elliott, Susan; Veugelers, Paul

2013-01-01

Background: This study examined differences in students' time spent in physical activity (PA) across secondary schools in rural, suburban, and urban environments and identified the environment-level factors associated with these between school differences in students' PA. Methods: Multilevel linear regression analyses were used to examine the…

A Cross-National Study of the Learning Environment in Chemistry Classes at Albanian, Kosovar, Romanian and Turkish Secondary Schools

ERIC Educational Resources Information Center

Emilov, Iliya; Tafrova-Grigorova, Adriana

2016-01-01

This study is part of a cross-national research entitled "In the past and now: Constructivist practices in teaching chemistry--Bulgaria, the Balkans and Europe." The purpose of the research is to explore science secondary classroom environments in terms of the constructivist approach. The study has been carried out at international…

40 CFR 50.6 - National primary and secondary ambient air quality standards for PM10.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 2 2010-07-01 2010-07-01 false National primary and secondary ambient... AGENCY (CONTINUED) AIR PROGRAMS NATIONAL PRIMARY AND SECONDARY AMBIENT AIR QUALITY STANDARDS § 50.6 National primary and secondary ambient air quality standards for PM10. (a) The level of the national...

40 CFR 50.7 - National primary and secondary ambient air quality standards for PM2.5.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 2 2010-07-01 2010-07-01 false National primary and secondary ambient... AGENCY (CONTINUED) AIR PROGRAMS NATIONAL PRIMARY AND SECONDARY AMBIENT AIR QUALITY STANDARDS § 50.7 National primary and secondary ambient air quality standards for PM2.5. (a) The national primary and...

40 CFR 50.13 - National primary and secondary ambient air quality standards for PM2.5.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 2 2010-07-01 2010-07-01 false National primary and secondary ambient... PROTECTION AGENCY (CONTINUED) AIR PROGRAMS NATIONAL PRIMARY AND SECONDARY AMBIENT AIR QUALITY STANDARDS § 50.13 National primary and secondary ambient air quality standards for PM2.5. (a) The national primary...

Low pressure-induced secondary structure transitions of regenerated silk fibroin in its wet film studied by time-resolved infrared spectroscopy.

PubMed

He, Zhipeng; Liu, Zhao; Zhou, Xiaofeng; Huang, He

2018-06-01

The secondary structure transitions of regenerated silk fibroin (RSF) under different external perturbations have been studied extensively, except for pressure. In this work, time-resolved infrared spectroscopy with the attenuated total reflectance (ATR) accessory was employed to follow the secondary structure transitions of RSF in its wet film under low pressure. It has been found that pressure alone is favorable only to the formation of β-sheet structure. Under constant pressure there is an optimum amount of D 2 O in the wet film (D 2 O : film = 2:1) so as to provide the optimal condition for the reorganization of the secondary structure and to have the largest formation of β-sheet structure. Under constant amount of D 2 O and constant pressure, the secondary structure transitions of RSF in its wet film can be divided into three stages along with time. In the first stage, random coil, α-helix, and β-turn were quickly transformed into β-sheet. In the second stage, random coil and β-turn were relatively slowly transformed into β-sheet and α-helix, and the content of α-helix was recovered to the value prior to the application of pressure. In the third and final stage, no measurable changes can be found for each secondary structure. This study may be helpful to understand the secondary structure changes of silk fibroin in silkworm's glands under hydrostatic pressure. © 2018 Wiley Periodicals, Inc.

Solution structural ensembles of substrate-free cytochrome P450(cam).

PubMed

Asciutto, Eliana K; Young, Matthew J; Madura, Jeffry; Pochapsky, Susan Sondej; Pochapsky, Thomas C

2012-04-24

Removal of substrate (+)-camphor from the active site of cytochrome P450(cam) (CYP101A1) results in nuclear magnetic resonance-detected perturbations in multiple regions of the enzyme. The (1)H-(15)N correlation map of substrate-free diamagnetic Fe(II) CO-bound CYP101A permits these perturbations to be mapped onto the solution structure of the enzyme. Residual dipolar couplings (RDCs) were measured for (15)N-(1)H amide pairs in two independent alignment media for the substrate-free enzyme and used as restraints in solvated molecular dynamics (MD) simulations to generate an ensemble of best-fit structures of the substrate-free enzyme in solution. Nuclear magnetic resonance-detected chemical shift perturbations reflect changes in the electronic environment of the NH pairs, such as hydrogen bonding and ring current shifts, and are observed for residues in the active site as well as in hinge regions between secondary structural features. RDCs provide information about relative orientations of secondary structures, and RDC-restrained MD simulations indicate that portions of a β-rich region adjacent to the active site shift so as to partially occupy the vacancy left by removal of the substrate. The accessible volume of the active site is reduced in the substrate-free enzyme relative to the substrate-bound structure calculated using the same methods. Both symmetric and asymmetric broadening of multiple resonances observed upon substrate removal as well as localized increased errors in RDC fits suggest that an ensemble of enzyme conformations are present in the substrate-free form.

Dynamic changes in the population structure of Escherichia coli in the Yeongsan River basin of South Korea.

PubMed

Jang, Jeonghwan; Di, Doris Y W; Han, Dukki; Unno, Tatsuya; Lee, Jeom-Ho; Sadowsky, Michael J; Hur, Hor-Gil

2015-11-01

Although Escherichia coli has been used as an indicator to examine fecal contamination of aquatic environment, it also has been reported to become naturalized to secondary habitats, including soil, water and beach sand. A total of 2880 E. coli isolates obtained from surface water and sediment samples from the Yeongsan River in 2013 were genotyped by using the horizontal fluorophore-enhanced rep-PCR DNA fingerprinting technique. Although different E. coli genotypic groups were observed between surface water and sediments in the dry season, they were mingled and undifferentiated from each other in the rainy season. This indicates that there are frequent sediment resuspension events in the river basin. Moreover, the genotypic composition of the E. coli population in the Yeongsan River basin changes over months and years, implying that genotypic structure of E. coli populations dynamically fluctuates in the river environment. Consequently, our data suggests that the use of E. coli libraries for fecal source tracking needs to be reassessed to account for the changing structure of riverine E. coli populations. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Preliminary Assessment of Potential Habitat Composites' Durability when Exposed to a Long-Term Radiation Environment and Micrometeoroid Impacts

NASA Technical Reports Server (NTRS)

Rojdev, Kristina; Graves, Russell; Golden, John; Atwell, William; O'Rouke, Mary Jane; Hill, Charles; Alred, John

2011-01-01

NASA's exploration goals include extending human presence beyond low earth orbit (LEO). As a result, habitation for crew is a critical requirement for meeting this goal. However, habitats are very large structures that contain a multitude of subsystems to sustain human life over long-durations in space, and one of the key challenges has been keeping weight to a minimum in order to reduce costs. Thus, light-weight and multifunctional structural materials are of great interest for habitation. NASA has started studying polymeric composite materials as potential lightweight and multifunctional structural materials for use in long-duration spaceflight. However, little is known about the survivability of these materials when exposed to the space environment outside of LEO for long durations. Thus, a study has been undertaken to investigate the durability of composite materials when exposed to long-duration radiation. Furthermore, as an addition to the primary study, a secondary preliminary investigation has been started on the micrometeoroid and orbital debris (MMOD) susceptibility of these materials after radiation exposure. The combined effects of radiation and MMOD impacts are the focus of this paper.

Predicting the performance of a strategic alliance: an analysis of the Community Clinical Oncology Program.

PubMed Central

Kaluzny, A D; Lacey, L M; Warnecke, R; Hynes, D M; Morrissey, J; Ford, L; Sondik, E

1993-01-01

OBJECTIVE. This study is designed to examine the effects of environment and structure of the Community Clinical Oncology Program (CCOP) on performance as measured by patient accrual to National Cancer Institute (NCI)-approved treatment protocols. DATA SOURCES/STUDY SETTING. Data and analysis are part of a larger evaluation of the NCI Community Clinical Oncology Program during its second funding cycle, June 1987-May 1990. Data, taken from primary and secondary sources, included a survey of selected informants in CCOPs and research bases, CCOP grant applications, CCOP annual progress reports, and site visits to a subsample of CCOPs (N = 20) and research bases (N = 5). Accrual data were obtained from NCI records. STUDY DESIGN. Analysis involved three complementary sets of factors: the local health care resources environment available to the CCOP, the larger policy environment as reflected by the relationship of the CCOP to selected research bases and the NCI, and the operational structure of the CCOP itself. A hierarchical model examined the separate and cumulative effects of local and policy environment and structure on performance. PRINCIPAL FINDINGS. Other things equal, the primary predictors of treatment accrual were: (1) the larger policy environment, as measured by the attendance of nurses at research base meetings; and (2) operational structure, as measured by the number and character of components within participating CCOPs and the number of hours per week worked by data managers. These factors explained 73 percent of the total variance in accrual performance. CONCLUSIONS. Findings suggest criteria for selecting the types of organizations to participate in the alliance, as well as for establishing guidelines for managing such alliances. A future challenge is to determine the extent to which factors predicting accrual to cancer treatment clinical trials are equally important as predictors of accrual to cancer prevention and control trials. PMID:8514498

Multitrait, Random Regression, or Simple Repeatability Model in High-Throughput Phenotyping Data Improve Genomic Prediction for Wheat Grain Yield.

PubMed

Sun, Jin; Rutkoski, Jessica E; Poland, Jesse A; Crossa, José; Jannink, Jean-Luc; Sorrells, Mark E

2017-07-01

High-throughput phenotyping (HTP) platforms can be used to measure traits that are genetically correlated with wheat ( L.) grain yield across time. Incorporating such secondary traits in the multivariate pedigree and genomic prediction models would be desirable to improve indirect selection for grain yield. In this study, we evaluated three statistical models, simple repeatability (SR), multitrait (MT), and random regression (RR), for the longitudinal data of secondary traits and compared the impact of the proposed models for secondary traits on their predictive abilities for grain yield. Grain yield and secondary traits, canopy temperature (CT) and normalized difference vegetation index (NDVI), were collected in five diverse environments for 557 wheat lines with available pedigree and genomic information. A two-stage analysis was applied for pedigree and genomic selection (GS). First, secondary traits were fitted by SR, MT, or RR models, separately, within each environment. Then, best linear unbiased predictions (BLUPs) of secondary traits from the above models were used in the multivariate prediction models to compare predictive abilities for grain yield. Predictive ability was substantially improved by 70%, on average, from multivariate pedigree and genomic models when including secondary traits in both training and test populations. Additionally, (i) predictive abilities slightly varied for MT, RR, or SR models in this data set, (ii) results indicated that including BLUPs of secondary traits from the MT model was the best in severe drought, and (iii) the RR model was slightly better than SR and MT models under drought environment. Copyright © 2017 Crop Science Society of America.

Untapped Resources: Biotechnological Potential of Peptides and Secondary Metabolites in Archaea

PubMed Central

Charlesworth, James C.; Burns, Brendan P.

2015-01-01

Archaea are an understudied domain of life often found in “extreme” environments in terms of temperature, salinity, and a range of other factors. Archaeal proteins, such as a wide range of enzymes, have adapted to function under these extreme conditions, providing biotechnology with interesting activities to exploit. In addition to producing structural and enzymatic proteins, archaea also produce a range of small peptide molecules (such as archaeocins) and other novel secondary metabolites such as those putatively involved in cell communication (acyl homoserine lactones), which can be exploited for biotechnological purposes. Due to the wide array of metabolites produced there is a great deal of biotechnological potential from antimicrobials such as diketopiperazines and archaeocins, as well as roles in the cosmetics and food industry. In this review we will discuss the diversity of small molecules, both peptide and nonpeptide, produced by archaea and their potential biotechnological applications. PMID:26504428

The foodscape: classification and field validation of secondary data sources.

PubMed

Lake, Amelia A; Burgoine, Thomas; Greenhalgh, Fiona; Stamp, Elaine; Tyrrell, Rachel

2010-07-01

The aims were to: develop a food environment classification tool and to test the acceptability and validity of three secondary sources of food environment data within a defined urban area of Newcastle-Upon-Tyne, using a field validation method. A 21 point (with 77 sub-categories) classification tool was developed. The fieldwork recorded 617 establishments selling food and/or food products. The sensitivity analysis of the secondary sources against fieldwork for the Newcastle City Council data was good (83.6%), while Yell.com and the Yellow Pages were low (51.2% and 50.9%, respectively). To improve the quality of secondary data, multiple sources should be used in order to achieve a realistic picture of the foodscape. 2010 Elsevier Ltd. All rights reserved.

The Ramachandran Number: An Order Parameter for Protein Geometry

DOE PAGES

Mannige, Ranjan V.; Kundu, Joyjit; Whitelam, Stephen; ...

2016-08-04

Three-dimensional protein structures usually contain regions of local order, called secondary structure, such as α-helices and β-sheets. Secondary structure is characterized by the local rotational state of the protein backbone, quantified by two dihedral angles called Øand Ψ. Particular types of secondary structure can generally be described by a single (diffuse) location on a two-dimensional plot drawn in the space of the angles Ø andΨ, called a Ramachandran plot. By contrast, a recently-discovered nanomaterial made from peptoids, structural isomers of peptides, displays a secondary-structure motif corresponding to two regions on the Ramachandran plot [Mannige et al., Nature 526, 415 (2015)].more » In order to describe such 'higher-order' secondary structure in a compact way we introduce here a means of describing regions on the Ramachandran plot in terms of a single Ramachandran number, R, which is a structurally meaningful combination of Ø andΨ. We show that the potential applications of R are numerous: it can be used to describe the geometric content of protein structures, and can be used to draw diagrams that reveal, at a glance, the frequency of occurrence of regular secondary structures and disordered regions in large protein datasets. We propose that R might be used as an order parameter for protein geometry for a wide range of applications.« less

Sixty-five years of the long march in protein secondary structure prediction: the final stretch?

PubMed Central

Yang, Yuedong; Gao, Jianzhao; Wang, Jihua; Heffernan, Rhys; Hanson, Jack; Paliwal, Kuldip; Zhou, Yaoqi

2018-01-01

Abstract Protein secondary structure prediction began in 1951 when Pauling and Corey predicted helical and sheet conformations for protein polypeptide backbone even before the first protein structure was determined. Sixty-five years later, powerful new methods breathe new life into this field. The highest three-state accuracy without relying on structure templates is now at 82–84%, a number unthinkable just a few years ago. These improvements came from increasingly larger databases of protein sequences and structures for training, the use of template secondary structure information and more powerful deep learning techniques. As we are approaching to the theoretical limit of three-state prediction (88–90%), alternative to secondary structure prediction (prediction of backbone torsion angles and Cα-atom-based angles and torsion angles) not only has more room for further improvement but also allows direct prediction of three-dimensional fragment structures with constantly improved accuracy. About 20% of all 40-residue fragments in a database of 1199 non-redundant proteins have <6 Å root-mean-squared distance from the native conformations by SPIDER2. More powerful deep learning methods with improved capability of capturing long-range interactions begin to emerge as the next generation of techniques for secondary structure prediction. The time has come to finish off the final stretch of the long march towards protein secondary structure prediction. PMID:28040746

Protein Structure Prediction by Protein Threading

NASA Astrophysics Data System (ADS)

Xu, Ying; Liu, Zhijie; Cai, Liming; Xu, Dong

The seminal work of Bowie, Lüthy, and Eisenberg (Bowie et al., 1991) on "the inverse protein folding problem" laid the foundation of protein structure prediction by protein threading. By using simple measures for fitness of different amino acid types to local structural environments defined in terms of solvent accessibility and protein secondary structure, the authors derived a simple and yet profoundly novel approach to assessing if a protein sequence fits well with a given protein structural fold. Their follow-up work (Elofsson et al., 1996; Fischer and Eisenberg, 1996; Fischer et al., 1996a,b) and the work by Jones, Taylor, and Thornton (Jones et al., 1992) on protein fold recognition led to the development of a new brand of powerful tools for protein structure prediction, which we now term "protein threading." These computational tools have played a key role in extending the utility of all the experimentally solved structures by X-ray crystallography and nuclear magnetic resonance (NMR), providing structural models and functional predictions for many of the proteins encoded in the hundreds of genomes that have been sequenced up to now.

Soft actuators and soft actuating devices

DOEpatents

Yang, Dian; Whitesides, George M.

2017-10-17

A soft buckling linear actuator is described, including: a plurality of substantially parallel bucklable, elastic structural components each having its longest dimension along a first axis; and a plurality of secondary structural components each disposed between and bridging two adjacent bucklable, elastic structural components; wherein every two adjacent bucklable, elastic structural components and the secondary structural components in-between define a layer comprising a plurality of cells each capable of being connected with a fluid inflation or deflation source; the secondary structural components from two adjacent layers are not aligned along a second axis perpendicular to the first axis; and the secondary structural components are configured not to buckle, the bucklable, elastic structural components are configured to buckle along the second axis to generate a linear force, upon the inflation or deflation of the cells. Methods of actuation using the same are also described.

Free energy minimization to predict RNA secondary structures and computational RNA design.

PubMed

Churkin, Alexander; Weinbrand, Lina; Barash, Danny

2015-01-01

Determining the RNA secondary structure from sequence data by computational predictions is a long-standing problem. Its solution has been approached in two distinctive ways. If a multiple sequence alignment of a collection of homologous sequences is available, the comparative method uses phylogeny to determine conserved base pairs that are more likely to form as a result of billions of years of evolution than by chance. In the case of single sequences, recursive algorithms that compute free energy structures by using empirically derived energy parameters have been developed. This latter approach of RNA folding prediction by energy minimization is widely used to predict RNA secondary structure from sequence. For a significant number of RNA molecules, the secondary structure of the RNA molecule is indicative of its function and its computational prediction by minimizing its free energy is important for its functional analysis. A general method for free energy minimization to predict RNA secondary structures is dynamic programming, although other optimization methods have been developed as well along with empirically derived energy parameters. In this chapter, we introduce and illustrate by examples the approach of free energy minimization to predict RNA secondary structures.

Effect of centrifugal forces on formation of secondary flow structures in a 180-degree curved artery model under pulsatile inflow conditions

NASA Astrophysics Data System (ADS)

Callahan, Shannon; Sajjad, Roshan; Bulusu, Kartik V.; Plesniak, Michael W.

2013-11-01

An experimental investigation of secondary flow structures within a 180-degree bent tube model of a curved artery was performed using phase-averaged, two-component, two-dimensional, particle image velocimetry (2C-2D PIV) under pulsatile inflow conditions. Pulsatile waveforms ranging from simple sinusoidal to physiological inflows were supplied. We developed a novel continuous wavelet transform algorithm (PIVlet 1.2) and applied it to vorticity fields for coherent secondary flow structure detection. Regime maps of secondary flow structures revealed new, deceleration-phase-dependent flow morphologies. The temporal instances where streamwise centrifugal forces dominated were associated with large-scale coherent structures, such as deformed Dean-, Lyne- and Wall-type (D-L-W) vortical structures. Magnitudes of streamwise and cross-stream centrifugal forces tend to balance during deceleration phases. Deceleration events were also associated with spatial reorganization and asymmetry in large-scale D-L-W secondary flow structures. Hence, the interaction between streamwise and cross-stream centrifugal forces that affects secondary flow morphologies is explained using a ``residual force'' parameter i.e., the difference in magnitudes of these forces. Supported by the NSF Grant No. CBET- 0828903 and GW Center for Biomimetics and Bioinspired Engineering.

Toward the fourth dimension of membrane protein structure: insight into dynamics from spin-labeling EPR spectroscopy.

PubMed

McHaourab, Hassane S; Steed, P Ryan; Kazmier, Kelli

2011-11-09

Trapping membrane proteins in the confines of a crystal lattice obscures dynamic modes essential for interconversion between multiple conformations in the functional cycle. Moreover, lattice forces could conspire with detergent solubilization to stabilize a minor conformer in an ensemble thus confounding mechanistic interpretation. Spin labeling in conjunction with electron paramagnetic resonance (EPR) spectroscopy offers an exquisite window into membrane protein dynamics in the native-like environment of a lipid bilayer. Systematic application of spin labeling and EPR identifies sequence-specific secondary structures, defines their topology and their packing in the tertiary fold. Long range distance measurements (60 Å-80 Å) between pairs of spin labels enable quantitative analysis of equilibrium dynamics and triggered conformational changes. This review highlights the contribution of spin labeling to bridging structure and mechanism. Efforts to develop methods for determining structures from EPR restraints and to increase sensitivity and throughput promise to expand spin labeling applications in membrane protein structural biology. Copyright © 2011 Elsevier Ltd. All rights reserved.

Evidence for validity of five secondary data sources for enumerating retail food outlets in seven American Indian communities in North Carolina.

PubMed

Fleischhacker, Sheila E; Rodriguez, Daniel A; Evenson, Kelly R; Henley, Amanda; Gizlice, Ziya; Soto, Dolly; Ramachandran, Gowri

2012-11-22

Most studies on the local food environment have used secondary sources to describe the food environment, such as government food registries or commercial listings (e.g., Reference USA). Most of the studies exploring evidence for validity of secondary retail food data have used on-site verification and have not conducted analysis by data source (e.g., sensitivity of Reference USA) or by food outlet type (e.g., sensitivity of Reference USA for convenience stores). Few studies have explored the food environment in American Indian communities. To advance the science on measuring the food environment, we conducted direct, on-site observations of a wide range of food outlets in multiple American Indian communities, without a list guiding the field observations, and then compared our findings to several types of secondary data. Food outlets located within seven State Designated Tribal Statistical Areas in North Carolina (NC) were gathered from online Yellow Pages, Reference USA, Dun & Bradstreet, local health departments, and the NC Department of Agriculture and Consumer Services. All TIGER/Line 2009 roads (>1,500 miles) were driven in six of the more rural tribal areas and, for the largest tribe, all roads in two of its cities were driven. Sensitivity, positive predictive value, concordance, and kappa statistics were calculated to compare secondary data sources to primary data. 699 food outlets were identified during primary data collection. Match rate for primary data and secondary data differed by type of food outlet observed, with the highest match rates found for grocery stores (97%), general merchandise stores (96%), and restaurants (91%). Reference USA exhibited almost perfect sensitivity (0.89). Local health department data had substantial sensitivity (0.66) and was almost perfect when focusing only on restaurants (0.91). Positive predictive value was substantial for Reference USA (0.67) and moderate for local health department data (0.49). Evidence for validity was comparatively lower for Dun & Bradstreet, online Yellow Pages, and the NC Department of Agriculture. Secondary data sources both over- and under-represented the food environment; they were particularly problematic for identifying convenience stores and specialty markets. More attention is needed to improve the validity of existing data sources, especially for rural local food environments.

Evidence for validity of five secondary data sources for enumerating retail food outlets in seven American Indian Communities in North Carolina

PubMed Central

2012-01-01

Background Most studies on the local food environment have used secondary sources to describe the food environment, such as government food registries or commercial listings (e.g., Reference USA). Most of the studies exploring evidence for validity of secondary retail food data have used on-site verification and have not conducted analysis by data source (e.g., sensitivity of Reference USA) or by food outlet type (e.g., sensitivity of Reference USA for convenience stores). Few studies have explored the food environment in American Indian communities. To advance the science on measuring the food environment, we conducted direct, on-site observations of a wide range of food outlets in multiple American Indian communities, without a list guiding the field observations, and then compared our findings to several types of secondary data. Methods Food outlets located within seven State Designated Tribal Statistical Areas in North Carolina (NC) were gathered from online Yellow Pages, Reference USA, Dun & Bradstreet, local health departments, and the NC Department of Agriculture and Consumer Services. All TIGER/Line 2009 roads (>1,500 miles) were driven in six of the more rural tribal areas and, for the largest tribe, all roads in two of its cities were driven. Sensitivity, positive predictive value, concordance, and kappa statistics were calculated to compare secondary data sources to primary data. Results 699 food outlets were identified during primary data collection. Match rate for primary data and secondary data differed by type of food outlet observed, with the highest match rates found for grocery stores (97%), general merchandise stores (96%), and restaurants (91%). Reference USA exhibited almost perfect sensitivity (0.89). Local health department data had substantial sensitivity (0.66) and was almost perfect when focusing only on restaurants (0.91). Positive predictive value was substantial for Reference USA (0.67) and moderate for local health department data (0.49). Evidence for validity was comparatively lower for Dun & Bradstreet, online Yellow Pages, and the NC Department of Agriculture. Conclusions Secondary data sources both over- and under-represented the food environment; they were particularly problematic for identifying convenience stores and specialty markets. More attention is needed to improve the validity of existing data sources, especially for rural local food environments. PMID:23173781

PreSSAPro: a software for the prediction of secondary structure by amino acid properties.

PubMed

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

2007-10-01

PreSSAPro is a software, available to the scientific community as a free web service designed to provide predictions of secondary structures starting from the amino acid sequence of a given protein. Predictions are based on our recently published work on the amino acid propensities for secondary structures in either large but not homogeneous protein data sets, as well as in smaller but homogeneous data sets corresponding to protein structural classes, i.e. all-alpha, all-beta, or alpha-beta proteins. Predictions result improved by the use of propensities evaluated for the right protein class. PreSSAPro predicts the secondary structure according to the right protein class, if known, or gives a multiple prediction with reference to the different structural classes. The comparison of these predictions represents a novel tool to evaluate what sequence regions can assume different secondary structures depending on the structural class assignment, in the perspective of identifying proteins able to fold in different conformations. The service is available at the URL http://bioinformatica.isa.cnr.it/PRESSAPRO/.

Students' perception of school environment and life satisfaction at Sinhala-medium secondary schools in the Colombo District, Sri Lanka.

PubMed

Nonaka, Daisuke; Gunawardena, Nalika S; Indrawansa, Susantha; Nanri, Akiko; Rajapakse, Lalini; Mizoue, Tetsuya; Samarasinghe, Diyanath

2012-11-01

The objective of this study was to examine the associations between students' perception of physical and psychosocial school environment and satisfaction with life among secondary school students in Colombo District, Sri Lanka. Data were collected from 20 Sinhala-medium secondary schools between January and February in 2010. A questionnaire-based survey was conducted with students in grade seven (n = 342) and grade ten (n = 446). Multivariate logistic regression analysis, adjusted for confounding variables, was used to assess the associations between students'satisfaction with life measured by Cantril ladders, and scores of perceived physical and psychosocial school environment that focused on school cleanliness and attractiveness, relations with teachers and peers, satisfaction with school and bullying. Students in the highest quartile of school environment score were significantly more likely to have high life satisfaction, compared to those in the lowest quartile (adjusted odds ratio 2.32; 95% confidence interval 1.35-3.99). Odds ratio of high life satisfaction increased with increasing school environment scores (p for trend<0.001). In conclusion, students who perceived positive school environment were significantly more likely to have high life satisfaction. Positive changes in the focused areas of school environment have the potential to lead to improved life satisfaction of students.

School grounds and physical activity: Associations at secondary schools, and over the transition from primary to secondary schools.

PubMed

Harrison, Flo; van Sluijs, Esther M F; Corder, Kirsten; Jones, Andy

2016-05-01

This paper aims to further understanding of the physical environments of secondary schools and their associations with young peoples' physical activity. Accelerometer-derived physical activity measurements from 299 participants in the SPEEDY study (Norfolk, UK) were obtained from baseline measurements (age 9-10y) and +4y follow-up. These were linked to objective measures of primary and secondary school environments as measured by the SPEEDY grounds audit tool. We saw considerable differences in the nature of school grounds between primary and secondary schools. Cross-sectional associations were seen between active travel provision scores and commuting time moderate-to-vigorous physical activity (MVPA) for 13-14 year old boys and adolescents living further from school. However, few associations were seen between changes in school grounds scores and changes in school-based MVPA. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Finding the target sites of RNA-binding proteins

PubMed Central

Li, Xiao; Kazan, Hilal; Lipshitz, Howard D; Morris, Quaid D

2014-01-01

RNA–protein interactions differ from DNA–protein interactions because of the central role of RNA secondary structure. Some RNA-binding domains (RBDs) recognize their target sites mainly by their shape and geometry and others are sequence-specific but are sensitive to secondary structure context. A number of small- and large-scale experimental approaches have been developed to measure RNAs associated in vitro and in vivo with RNA-binding proteins (RBPs). Generalizing outside of the experimental conditions tested by these assays requires computational motif finding. Often RBP motif finding is done by adapting DNA motif finding methods; but modeling secondary structure context leads to better recovery of RBP-binding preferences. Genome-wide assessment of mRNA secondary structure has recently become possible, but these data must be combined with computational predictions of secondary structure before they add value in predicting in vivo binding. There are two main approaches to incorporating structural information into motif models: supplementing primary sequence motif models with preferred secondary structure contexts (e.g., MEMERIS and RNAcontext) and directly modeling secondary structure recognized by the RBP using stochastic context-free grammars (e.g., CMfinder and RNApromo). The former better reconstruct known binding preferences for sequence-specific RBPs but are not suitable for modeling RBPs that recognize shape and geometry of RNAs. Future work in RBP motif finding should incorporate interactions between multiple RBDs and multiple RBPs in binding to RNA. WIREs RNA 2014, 5:111–130. doi: 10.1002/wrna.1201 PMID:24217996

Challenges of Formulation of Strategic Plans in Secondary Schools in Kenya: A Case of Mombasa County and Its Environs

ERIC Educational Resources Information Center

Nyagah, Agnes S. M.

2015-01-01

The study is aimed at analyzing the factors that affect formulation of strategic plans in secondary schools in Mombasa County and its environs. The study looks at various variables namely leadership, training, resources allocation and education policy frameworks as the main challenges. The paper concludes that the above variables to a large extent…

The Effect of 3D Virtual Learning Environment on Secondary School Third Grade Students' Attitudes toward Mathematics

ERIC Educational Resources Information Center

Simsek, Irfan

2016-01-01

With this research, in Second Life environment which is a three dimensional online virtual world, it is aimed to reveal the effects of student attitudes toward mathematics courses and design activities which will enable the third grade students of secondary school (primary education seventh grade) to see the 3D objects in mathematics courses in a…

Structural diversity of domain superfamilies in the CATH database.

PubMed

Reeves, Gabrielle A; Dallman, Timothy J; Redfern, Oliver C; Akpor, Adrian; Orengo, Christine A

2006-07-14

The CATH database of domain structures has been used to explore the structural variation of homologous domains in 294 well populated domain structure superfamilies, each containing at least three sequence diverse relatives. Our analyses confirm some previously detected trends relating sequence divergence to structural variation but for a much larger dataset and in some superfamilies the new data reveal exceptional structural variation. Use of a new algorithm (2DSEC) to analyse variability in secondary structure compositions across a superfamily sheds new light on how structures evolve. 2DSEC detects inserted secondary structures that embellish the core of conserved secondary structures found throughout the superfamily. Analysis showed that for 56% of highly populated superfamilies (>9 sequence diverse relatives), there are twofold or more increases in the numbers of secondary structures in some relatives. In some families fivefold increases occur, sometimes modifying the fold of the domain. Manual inspection of secondary structure insertions or embellishments in 48 particularly variable superfamilies revealed that although these insertions were usually discontiguous in the sequence they were often co-located in 3D resulting in a larger structural motif that often modified the geometry of the active site or the surface conformation promoting diverse domain partnerships and protein interactions. These observations, supported by automatic analysis of all well populated CATH families, suggest that accretion of small secondary structure insertions may provide a simple mechanism for evolving new functions in diverse relatives. Some layered domain architectures (e.g. mainly-beta and alpha-beta sandwiches) that recur highly in the genomes more frequently exploit these types of embellishments to modify function. In these architectures, aggregation occurs most often at the edges, top or bottom of the beta-sheets. Information on structural variability across domain superfamilies has been made available through the CATH Dictionary of Homologous Structures (DHS).

RNA secondary structure prediction with pseudoknots: Contribution of algorithm versus energy model.

PubMed

Jabbari, Hosna; Wark, Ian; Montemagno, Carlo

2018-01-01

RNA is a biopolymer with various applications inside the cell and in biotechnology. Structure of an RNA molecule mainly determines its function and is essential to guide nanostructure design. Since experimental structure determination is time-consuming and expensive, accurate computational prediction of RNA structure is of great importance. Prediction of RNA secondary structure is relatively simpler than its tertiary structure and provides information about its tertiary structure, therefore, RNA secondary structure prediction has received attention in the past decades. Numerous methods with different folding approaches have been developed for RNA secondary structure prediction. While methods for prediction of RNA pseudoknot-free structure (structures with no crossing base pairs) have greatly improved in terms of their accuracy, methods for prediction of RNA pseudoknotted secondary structure (structures with crossing base pairs) still have room for improvement. A long-standing question for improving the prediction accuracy of RNA pseudoknotted secondary structure is whether to focus on the prediction algorithm or the underlying energy model, as there is a trade-off on computational cost of the prediction algorithm versus the generality of the method. The aim of this work is to argue when comparing different methods for RNA pseudoknotted structure prediction, the combination of algorithm and energy model should be considered and a method should not be considered superior or inferior to others if they do not use the same scoring model. We demonstrate that while the folding approach is important in structure prediction, it is not the only important factor in prediction accuracy of a given method as the underlying energy model is also as of great value. Therefore we encourage researchers to pay particular attention in comparing methods with different energy models.

Self-Efficacy, School Resources, Job Stressors and Burnout among Spanish Primary and Secondary School Teachers: A Structural Equation Approach

ERIC Educational Resources Information Center

Betoret, Fernando Domenech

2009-01-01

This study examines the relationship between school resources, teacher self-efficacy, potential multi-level stressors and teacher burnout using structural equation modelling. The causal structure for primary and secondary school teachers was also examined. The sample was composed of 724 primary and secondary Spanish school teachers. The changes…

Catalytically active alkaline molten globular enzyme: Effect of pH and temperature on the structural integrity of 5-aminolevulinate synthase*

PubMed Central

Stojanovski, Bosko M.; Breydo, Leonid; Hunter, Gregory A.; Uversky, Vladimir N.; Ferreira, Gloria C.

2014-01-01

5-Aminolevulinate synthase (ALAS), a pyridoxal-5′phosphate (PLP)-dependent enzyme, catalyzes the first step of heme biosynthesis in mammals. Circular dichroism (CD) and fluorescence spectroscopies were used to examine the effects of pH (1.0–3.0 and 7.5–10.5) and temperature (20 and 37 °C) on the structural integrity of ALAS. The secondary structure, as deduced from far-UV CD, is mostly resilient to pH and temperature changes. Partial unfolding was observed at pH 2.0, but further decreasing pH resulted in acid-induced refolding of the secondary structure to nearly native levels. The tertiary structure rigidity, monitored by near-UV CD, is lost under acidic and specific alkaline conditions (pH 10.5 and pH 9.5/37 °C), where ALAS populates a molten globule state. As the enzyme becomes less structured with increased alkalinity, the chiral environment of the internal aldimine is also modified, with a shift from a 420 nm to 330 nm dichroic band. Under acidic conditions, the PLP cofactor dissociates from ALAS. Reaction with 8-anilino-1-naphtalenesulfonic acid corroborates increased exposure of hydrophobic clusters in the alkaline and acidic molten globules, although the reaction is more pronounced with the latter. Furthermore, quenching the intrinsic fluorescence of ALAS with acrylamide at pH 1.0 and 9.5 yielded subtly different dynamic quenching constants. The alkaline molten globule state of ALAS is catalytically active (pH 9.5/37 °C), although the kcat value is significantly decreased. Finally, the binding of 5-aminolevulinate restricts conformational fluctuations in the alkaline molten globule. Overall, our findings prove how the structural plasticity of ALAS contributes to reaching a functional enzyme. PMID:25240868

RNApdbee 2.0: multifunctional tool for RNA structure annotation.

PubMed

Zok, Tomasz; Antczak, Maciej; Zurkowski, Michal; Popenda, Mariusz; Blazewicz, Jacek; Adamiak, Ryszard W; Szachniuk, Marta

2018-04-30

In the field of RNA structural biology and bioinformatics, an access to correctly annotated RNA structure is of crucial importance, especially in the secondary and 3D structure predictions. RNApdbee webserver, introduced in 2014, primarily aimed to address the problem of RNA secondary structure extraction from the PDB files. Its new version, RNApdbee 2.0, is a highly advanced multifunctional tool for RNA structure annotation, revealing the relationship between RNA secondary and 3D structure given in the PDB or PDBx/mmCIF format. The upgraded version incorporates new algorithms for recognition and classification of high-ordered pseudoknots in large RNA structures. It allows analysis of isolated base pairs impact on RNA structure. It can visualize RNA secondary structures-including that of quadruplexes-with depiction of non-canonical interactions. It also annotates motifs to ease identification of stems, loops and single-stranded fragments in the input RNA structure. RNApdbee 2.0 is implemented as a publicly available webserver with an intuitive interface and can be freely accessed at http://rnapdbee.cs.put.poznan.pl/.

Cold Regime Interannual Variability of Primary and Secondary Producer Community Composition in the Southeastern Bering Sea

PubMed Central

Stauffer, Beth A.; Miksis-Olds, Jennifer; Goes, Joaquim I.

2015-01-01

Variability of hydrographic conditions and primary and secondary productivity between cold and warm climatic regimes in the Bering Sea has been the subject of much study in recent years, while interannual variability within a single regime and across multiple trophic levels has been less well-documented. Measurements from an instrumented mooring on the southeastern shelf of the Bering Sea were analyzed for the spring-to-summer transitions within the cold regime years of 2009–2012 to investigate the interannual variability of hydrographic conditions, primary producer biomass, and acoustically-derived secondary producer and consumer abundance and community structure. Hydrographic conditions in 2012 were significantly different than in 2009, 2010, and 2011, driven largely by increased ice extent and thickness, later ice retreat, and earlier stratification of the water column. Primary producer biomass was more tightly coupled to hydrographic conditions in 2012 than in 2009 or 2011, and shallow and mid-column phytoplankton blooms tended to occur independent of one another. There was a high degree of variability in the relationships between different classes of secondary producers and hydrographic conditions, evidence of significant intra-consumer interactions, and trade-offs between different consumer size classes in each year. Phytoplankton blooms stimulated different populations of secondary producers in each year, and summer consumer populations appeared to determine dominant populations in the subsequent spring. Overall, primary producers and secondary producers were more tightly coupled to each other and to hydrographic conditions in the coldest year compared to the warmer years. The highly variable nature of the interactions between the atmospherically-driven hydrographic environment, primary and secondary producers, and within food webs underscores the need to revisit how climatic regimes within the Bering Sea are defined and predicted to function given changing climate scenarios. PMID:26110822

Cold Regime interannual variability of primary and secondary producer community composition in the southeastern Bering Sea.

PubMed

Stauffer, Beth A; Miksis-Olds, Jennifer; Goes, Joaquim I

2015-01-01

Variability of hydrographic conditions and primary and secondary productivity between cold and warm climatic regimes in the Bering Sea has been the subject of much study in recent years, while interannual variability within a single regime and across multiple trophic levels has been less well-documented. Measurements from an instrumented mooring on the southeastern shelf of the Bering Sea were analyzed for the spring-to-summer transitions within the cold regime years of 2009-2012 to investigate the interannual variability of hydrographic conditions, primary producer biomass, and acoustically-derived secondary producer and consumer abundance and community structure. Hydrographic conditions in 2012 were significantly different than in 2009, 2010, and 2011, driven largely by increased ice extent and thickness, later ice retreat, and earlier stratification of the water column. Primary producer biomass was more tightly coupled to hydrographic conditions in 2012 than in 2009 or 2011, and shallow and mid-column phytoplankton blooms tended to occur independent of one another. There was a high degree of variability in the relationships between different classes of secondary producers and hydrographic conditions, evidence of significant intra-consumer interactions, and trade-offs between different consumer size classes in each year. Phytoplankton blooms stimulated different populations of secondary producers in each year, and summer consumer populations appeared to determine dominant populations in the subsequent spring. Overall, primary producers and secondary producers were more tightly coupled to each other and to hydrographic conditions in the coldest year compared to the warmer years. The highly variable nature of the interactions between the atmospherically-driven hydrographic environment, primary and secondary producers, and within food webs underscores the need to revisit how climatic regimes within the Bering Sea are defined and predicted to function given changing climate scenarios.

Secondary Structure Predictions for Long RNA Sequences Based on Inversion Excursions and MapReduce.

PubMed

Yehdego, Daniel T; Zhang, Boyu; Kodimala, Vikram K R; Johnson, Kyle L; Taufer, Michela; Leung, Ming-Ying

2013-05-01

Secondary structures of ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation. Experimental observations and computing limitations suggest that we can approach the secondary structure prediction problem for long RNA sequences by segmenting them into shorter chunks, predicting the secondary structures of each chunk individually using existing prediction programs, and then assembling the results to give the structure of the original sequence. The selection of cutting points is a crucial component of the segmenting step. Noting that stem-loops and pseudoknots always contain an inversion, i.e., a stretch of nucleotides followed closely by its inverse complementary sequence, we developed two cutting methods for segmenting long RNA sequences based on inversion excursions: the centered and optimized method. Each step of searching for inversions, chunking, and predictions can be performed in parallel. In this paper we use a MapReduce framework, i.e., Hadoop, to extensively explore meaningful inversion stem lengths and gap sizes for the segmentation and identify correlations between chunking methods and prediction accuracy. We show that for a set of long RNA sequences in the RFAM database, whose secondary structures are known to contain pseudoknots, our approach predicts secondary structures more accurately than methods that do not segment the sequence, when the latter predictions are possible computationally. We also show that, as sequences exceed certain lengths, some programs cannot computationally predict pseudoknots while our chunking methods can. Overall, our predicted structures still retain the accuracy level of the original prediction programs when compared with known experimental secondary structure.

Examining local-level factors shaping school nutrition policy implementation in Ontario, Canada.

PubMed

Vine, Michelle M; Elliott, Susan J

2014-06-01

Increasing numbers of overweight and obese youth draw attention to the school as an important setting for targeted nutrition interventions, given that it is where they spend a majority of their waking time. The objective of the present study was to explore local-level factors shaping the implementation of a school nutrition policy. In-depth, semi-structured interviews were conducted in person or via the telephone (a maximum of 60 min). An interview guide was informed by the Analysis Grid for Environments Linked to Obesity (ANGELO) framework, research objectives and literature. Key themes centred on policy implementation, including facilitators and barriers (i.e. resources, capacity), user satisfaction (i.e. students) and communication strategies. Secondary schools in Ontario, Canada. Twenty-two participants from local agencies supporting school nutrition programming (n 8) and secondary-school principals, vice principals and teachers (n 14) from nine schools across three Ontario school boards. Results are organized according to environments outlined in the ANGELO framework. The cost of healthy food for sale, revenue loss (economic), proximity of schools to off-site food outlets (physical), the restrictive nature of policy, the role of key stakeholders (political), the role of stigma and school culture (sociocultural) act as local-level barriers to policy implementation. Gaps in policy implementation include the high cost of food for sale and subsequent revenue generation, the close proximity of internal and external food environments, the need for consultation and communication between stakeholders, and strategies to reduce stigma and improve the school nutrition culture.

Biological Redox Cycling Of Iron In Nontronite And Its Potential Application In Nitrate Removal

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

Zhao, Linduo; Dong, Hailiang; Kukkadapu, Ravi K.

2015-05-05

Redox cycling of structural Fe in phyllosilicates provides a potential method to remediate nitrate contamination in natural environment. Past research has only studied chemical redox cycles or a single biologically mediated redox cycle of Fe in phyllosilicates. The objective of this research was to study three microbially driven redox cycles of Fe in one phyllosilicate, nontronite (NAu-2). During the reduction phase structural Fe(III) in NAu-2 served as electron acceptor, lactate as electron donor, AQDS as electron shuttle, and dissimilatory Fe(III)-reducing bacteria Shewanella putrefaciens CN32 as mediator in bicarbonate-buffered and PIPES-buffered media. During the oxidation phase, biogenic Fe(II) served an electronmore » donor, nitrate as electron acceptor, and nitrate-dependent Fe(II)-oxidizing bacteria Pseudogulbenkiania sp. strain 2002 as mediator in the same media. For all three cycles, structural Fe in NAu-2 was able to reversibly undergo 3 redox cycles without significant reductive or oxidative dissolution. X-ray diffraction and scanning and transmission electron microscopy revealed that NAu-2 was the dominant residual mineral throughout the 3 redox cycles with some dissolution textures but no significant secondary mineralization. Mössbauer spectroscopy revealed that Fe(II) in bio-reduced samples likely occurred in two distinct environments, at edges and the interior of the NAu-2 structure. Nitrate was completely reduced to nitrogen gas under both buffer conditions and this extent and rate did not change with Fe redox cycles. Mössbauer spectroscopy further revealed that nitrate reduction was coupled to predominant/preferred oxidation of edge Fe(II). These results suggest that structural Fe in phyllosilicates may represent a renewable source to continuously remove nitrate in natural environments.« less

Variability in secondary structure of 18S ribosomal RNA as topological marker for identification of Paramecium species.

PubMed

Shakoori, Farah R; Tasneem, Fareeda; Al-Ghanim, K; Mahboob, S; Al-Misned, F; Jahan, Nusrat; Shakoori, Abdul Rauf

2014-12-01

Besides cytological and molecular applications, Paramecium is being used in water quality assessment and for determination of saprobic levels. An unambiguous identification of these unicellular eukaryotes is not only essential, but its ecological diversity must also be explored in the local environment. 18SrRNA genes of all the strains of Paramecium species isolated from waste water were amplified, cloned and sequenced. Phylogenetic comparison of the nucleotide sequences of these strains with 23 closely related Paramecium species from GenBank Database enabled identification of Paramecium multimicronucleatum and Paramecium jenningsi. Some isolates did not show significant close association with other Paramecium species, and because of their unique position in the phylogenetic tree, they were considered new to the field. In the present report, these isolates are being designated as Paramecium caudatum pakistanicus. In this article, secondary structure of 18SrRNA has also been analyzed as an additional and perhaps more reliable topological marker for species discrimination and for determining possible phylogenetic relationship between the ciliate species. On the basis of comparison of secondary structure of 18SrRNA of various isolated Paramacium strains, and among Paramecium caudatum pakistanicus, Tetrahymena thermophila, Drosophila melanogaster, and Homo sapiens, it can be deduced that variable regions are more helpful in differentiating the species at interspecific level rather than at intraspecific level. It was concluded that V3 was the least variable region in all the organisms, V2 and V7 were the longest expansion segments of D. melanogaster and there was continuous mutational bias towards G.C base pairing in H. sapiens. © 2014 Wiley Periodicals, Inc.

Density functional study of molecular interactions in secondary structures of proteins.

PubMed

Takano, Yu; Kusaka, Ayumi; Nakamura, Haruki

2016-01-01

Proteins play diverse and vital roles in biology, which are dominated by their three-dimensional structures. The three-dimensional structure of a protein determines its functions and chemical properties. Protein secondary structures, including α-helices and β-sheets, are key components of the protein architecture. Molecular interactions, in particular hydrogen bonds, play significant roles in the formation of protein secondary structures. Precise and quantitative estimations of these interactions are required to understand the principles underlying the formation of three-dimensional protein structures. In the present study, we have investigated the molecular interactions in α-helices and β-sheets, using ab initio wave function-based methods, the Hartree-Fock method (HF) and the second-order Møller-Plesset perturbation theory (MP2), density functional theory, and molecular mechanics. The characteristic interactions essential for forming the secondary structures are discussed quantitatively.

Pairwise amino acid secondary structural propensities

NASA Astrophysics Data System (ADS)

Chemmama, Ilan E.; Chapagain, Prem P.; Gerstman, Bernard S.

2015-04-01

We investigate the propensities for amino acids to form a specific secondary structure when they are paired with other amino acids. Our investigations use molecular dynamics (MD) computer simulations, and we compare the results to those from the Protein Data Bank (PDB). Proper comparison requires weighting of the MD results in a manner consistent with the relative frequency of appearance in the PDB of each possible pair of amino acids. We find that the propensity for an amino acid to assume a secondary structure varies dramatically depending on the amino acid that is before or after it in the primary sequence. This cooperative effect means that when selecting amino acids to facilitate the formation of a secondary structure in peptide engineering experiments, the adjacent amino acids must be considered. We also examine the preference for a secondary structure in bacterial proteins and compare the results to those of human proteins.

The reliability of molecular dynamics simulations of the multidrug transporter P-glycoprotein in a membrane environment

PubMed Central

Condic-Jurkic, Karmen; Subramanian, Nandhitha; Mark, Alan E.

2018-01-01

Despite decades of research, the mechanism of action of the ABC multidrug transporter P-glycoprotein (P-gp) remains elusive. Due to experimental limitations, many researchers have turned to molecular dynamics simulation studies in order to investigate different aspects of P-gp function. However, such studies are challenging and caution is required when interpreting the results. P-gp is highly flexible and the time scale on which it can be simulated is limited. There is also uncertainty regarding the accuracy of the various crystal structures available, let alone the structure of the protein in a physiologically relevant environment. In this study, three alternative structural models of mouse P-gp (3G5U, 4KSB, 4M1M), all resolved to 3.8 Å, were used to initiate sets of simulations of P-gp in a membrane environment in order to determine: a) the sensitivity of the results to differences in the starting configuration; and b) the extent to which converged results could be expected on the times scales commonly simulated for this system. The simulations suggest that the arrangement of the nucleotide binding domains (NBDs) observed in the crystal structures is not stable in a membrane environment. In all simulations, the NBDs rapidly associated (within 10 ns) and changes within the transmembrane helices were observed. The secondary structure within the transmembrane domain was best preserved in the 4M1M model under the simulation conditions used. However, the extent to which replicate simulations diverged on a 100 to 200 ns timescale meant that it was not possible to draw definitive conclusions as to which structure overall was most stable, or to obtain converged and reliable results for any of the properties examined. The work brings into question the reliability of conclusions made in regard to the nature of specific interactions inferred from previous simulation studies on this system involving similar sampling times. It also highlights the need to demonstrate the statistical significance of any results obtained in simulations of large flexible proteins, especially where the initial structure is uncertain. PMID:29370310

The reliability of molecular dynamics simulations of the multidrug transporter P-glycoprotein in a membrane environment.

PubMed

Condic-Jurkic, Karmen; Subramanian, Nandhitha; Mark, Alan E; O'Mara, Megan L

2018-01-01

Despite decades of research, the mechanism of action of the ABC multidrug transporter P-glycoprotein (P-gp) remains elusive. Due to experimental limitations, many researchers have turned to molecular dynamics simulation studies in order to investigate different aspects of P-gp function. However, such studies are challenging and caution is required when interpreting the results. P-gp is highly flexible and the time scale on which it can be simulated is limited. There is also uncertainty regarding the accuracy of the various crystal structures available, let alone the structure of the protein in a physiologically relevant environment. In this study, three alternative structural models of mouse P-gp (3G5U, 4KSB, 4M1M), all resolved to 3.8 Å, were used to initiate sets of simulations of P-gp in a membrane environment in order to determine: a) the sensitivity of the results to differences in the starting configuration; and b) the extent to which converged results could be expected on the times scales commonly simulated for this system. The simulations suggest that the arrangement of the nucleotide binding domains (NBDs) observed in the crystal structures is not stable in a membrane environment. In all simulations, the NBDs rapidly associated (within 10 ns) and changes within the transmembrane helices were observed. The secondary structure within the transmembrane domain was best preserved in the 4M1M model under the simulation conditions used. However, the extent to which replicate simulations diverged on a 100 to 200 ns timescale meant that it was not possible to draw definitive conclusions as to which structure overall was most stable, or to obtain converged and reliable results for any of the properties examined. The work brings into question the reliability of conclusions made in regard to the nature of specific interactions inferred from previous simulation studies on this system involving similar sampling times. It also highlights the need to demonstrate the statistical significance of any results obtained in simulations of large flexible proteins, especially where the initial structure is uncertain.

Structure prediction of the second extracellular loop in G-protein-coupled receptors.

PubMed

Kmiecik, Sebastian; Jamroz, Michal; Kolinski, Michal

2014-06-03

G-protein-coupled receptors (GPCRs) play key roles in living organisms. Therefore, it is important to determine their functional structures. The second extracellular loop (ECL2) is a functionally important region of GPCRs, which poses significant challenge for computational structure prediction methods. In this work, we evaluated CABS, a well-established protein modeling tool for predicting ECL2 structure in 13 GPCRs. The ECL2s (with between 13 and 34 residues) are predicted in an environment of other extracellular loops being fully flexible and the transmembrane domain fixed in its x-ray conformation. The modeling procedure used theoretical predictions of ECL2 secondary structure and experimental constraints on disulfide bridges. Our approach yielded ensembles of low-energy conformers and the most populated conformers that contained models close to the available x-ray structures. The level of similarity between the predicted models and x-ray structures is comparable to that of other state-of-the-art computational methods. Our results extend other studies by including newly crystallized GPCRs. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Effect of homogenization and pasteurization on the structure and stability of whey protein in milk.

PubMed

Qi, Phoebe X; Ren, Daxi; Xiao, Yingping; Tomasula, Peggy M

2015-05-01

The effect of homogenization alone or in combination with high-temperature, short-time (HTST) pasteurization or UHT processing on the whey fraction of milk was investigated using highly sensitive spectroscopic techniques. In pilot plant trials, 1-L quantities of whole milk were homogenized in a 2-stage homogenizer at 35°C (6.9 MPa/10.3 MPa) and, along with skim milk, were subjected to HTST pasteurization (72°C for 15 s) or UHT processing (135°C for 2 s). Other whole milk samples were processed using homogenization followed by either HTST pasteurization or UHT processing. The processed skim and whole milk samples were centrifuged further to remove fat and then acidified to pH 4.6 to isolate the corresponding whey fractions, and centrifuged again. The whey fractions were then purified using dialysis and investigated using the circular dichroism, Fourier transform infrared, and Trp intrinsic fluorescence spectroscopic techniques. Results demonstrated that homogenization combined with UHT processing of milk caused not only changes in protein composition but also significant secondary structural loss, particularly in the amounts of apparent antiparallel β-sheet and α-helix, as well as diminished tertiary structural contact. In both cases of homogenization alone and followed by HTST treatments, neither caused appreciable chemical changes, nor remarkable secondary structural reduction. But disruption was evident in the tertiary structural environment of the whey proteins due to homogenization of whole milk as shown by both the near-UV circular dichroism and Trp intrinsic fluorescence. In-depth structural stability analyses revealed that even though processing of milk imposed little impairment on the secondary structural stability, the tertiary structural stability of whey protein was altered significantly. The following order was derived based on these studies: raw whole>HTST, homogenized, homogenized and pasteurized>skimmed and pasteurized, and skimmed UHT>homogenized UHT. The methodology demonstrated in this study can be used to gain insight into the behavior of milk proteins when processed and provides a new empirical and comparative approach for analyzing and assessing the effect of processing schemes on the nutrition and quality of milk and dairy product without the need for extended separation and purification, which can be both time-consuming and disruptive to protein structures. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Structural alterations in rat liver proteins due to streptozotocin-induced diabetes and the recovery effect of selenium: Fourier transform infrared microspectroscopy and neural network study

NASA Astrophysics Data System (ADS)

Bozkurt, Ozlem; Haman Bayari, Sevgi; Severcan, Mete; Krafft, Christoph; Popp, Jürgen; Severcan, Feride

2012-07-01

The relation between protein structural alterations and tissue dysfunction is a major concern as protein fibrillation and/or aggregation due to structural alterations has been reported in many disease states. In the current study, Fourier transform infrared microspectroscopic imaging has been used to investigate diabetes-induced changes on protein secondary structure and macromolecular content in streptozotocin-induced diabetic rat liver. Protein secondary structural alterations were predicted using neural network approach utilizing the amide I region. Moreover, the role of selenium in the recovery of diabetes-induced alterations on macromolecular content and protein secondary structure was also studied. The results revealed that diabetes induced a decrease in lipid to protein and glycogen to protein ratios in diabetic livers. Significant alterations in protein secondary structure were observed with a decrease in α-helical and an increase in β-sheet content. Both doses of selenium restored diabetes-induced changes in lipid to protein and glycogen to protein ratios. However, low-dose selenium supplementation was not sufficient to recover the effects of diabetes on protein secondary structure, while a higher dose of selenium fully restored diabetes-induced alterations in protein structure.

Adsorption of fibrinogen on a biomedical-grade stainless steel 316LVM surface: a PM-IRRAS study of the adsorption thermodynamics, kinetics and secondary structure changes.

PubMed

Desroches, Marie-Josee; Omanovic, Sasha

2008-05-14

Polarization-modulation infrared reflection-absorption spectroscopy (PM-IRRAS) was employed to investigate the interaction of serum protein fibrinogen with a biomedical-grade 316LVM stainless steel surface, in terms of the adsorption thermodynamics, kinetics and secondary structure changes of the protein. Apparent Gibbs energy of adsorption values indicated a highly spontaneous and strong adsorption of fibrinogen onto the surface. The kinetics of fibrinogen adsorption were successfully modeled using a pseudo first-order kinetic model. Deconvolution of the amide I bands indicated that the adsorption of fibrinogen on 316LVM results in significant changes in the protein's secondary structure that occur predominantly within the first minute of adsorption. Among the investigated structures, the alpha-helix structure undergoes the smallest changes, while the beta-sheet and beta-turns structures undergo significant changes. It was shown that lateral interactions between the adsorbed molecules do not play a role in controlling the secondary structure changes. An increase in temperature induced changes in the secondary structure of the protein, characterized by a loss of the alpha-helical content and its transformation into the beta-turns structure.

Feeding currents of the upside down jellyfish in the presence of background flow.

PubMed

Hamlet, Christina L; Miller, Laura A

2012-11-01

The upside-down jellyfish (Cassiopea spp.) is an ideal organism for examining feeding and exchange currents generated by bell pulsations due to its relatively sessile nature. Previous experiments and numerical simulations have shown that the oral arms play an important role in directing new fluid into the bell from along the substrate. All of this work, however, has considered the jellyfish in the absence of background flow, but the natural environments of Cassiopea and other cnidarians are dynamic. Flow velocities and directions fluctuate on multiple time scales, and mechanisms of particle capture may be fundamentally different in moving fluids. In this paper, the immersed boundary method is used to simulate a simplified jellyfish in flow. The elaborate oral arm structure is modeled as a homogenous porous layer. The results show that the oral arms trap vortices as they form during contraction and expansion of the bell. For constant flow conditions, the vortices are directed gently across the oral arms where particle capture occurs. For variable direction flows, the secondary structures change the overall pattern of the flow around the bell and appear to stabilize regions of mixing around the secondary mouths.

Ovarian structure and oogenesis of the extremophile viviparous teleost Poecilia mexicana (Poeciliidae) from an active sulfur spring cave in Southern Mexico.

PubMed

Torres-Martínez, Aarón; Hernández-Franyutti, Arlette; Uribe, Mari Carmen; Contreras-Sánchez, Wilfrido Miguel

2017-12-01

The structure of the ovary and oogenesis of Poecilia mexicana from an active sulfur spring cave is documented. Poecilia mexicana is the only poeciliid adapted to a subterranean environment with high hydrogen sulfide levels and extreme hypoxic conditions. Twenty females were captured throughout one year at Cueva del Azufre, located in the State of Tabasco in Southern Mexico. Ovaries were processed with histological techniques. P. mexicana has a single, ovoid ovary with ovigerous lamella that project to the ovarian lumen. The ovarian wall presents abundant loose connective tissue, numerous melanomacrophage centers and large blood vessels, possibly associated with hypoxic conditions. The germinal epithelium bordering the ovarian lumen contains somatic and germ cells forming cell nests projecting into the stroma. P. mexicana stores sperm in ovarian folds associated with follicles at different developmental phases. Oogenesis in P. mexicana consisted of the following stages: (i) oogonial proliferation, (ii) chromatin nucleolus, (iii) primary growth, subdivided into: (a) one nucleolus, (b) multiple nucleoli, (c) droplet oils-cortical alveoli steps; (iv) secondary growth, subdivided in: (a) early secondary growth, (b) late secondary growth, and (c) full grown. Follicular atresia was present in all stages of follicular development; it was characterized by oocyte degeneration, where follicle cells hypertrophy and differentiate in phagocytes. The ovary and oogenesis are similar to these seen in other poeciliids, but we found frequent atretic follicles, melanomacrophage centers, reduced fecundity and increased of offspring size. © 2017 Wiley Periodicals, Inc.

A comparative study on the clinical decision-making processes of nurse practitioners vs. medical doctors using scenarios in a secondary care environment.

PubMed

Thompson, Stephen; Moorley, Calvin; Barratt, Julian

2017-05-01

To investigate the decision-making skills of secondary care nurse practitioners compared with those of medical doctors. A literature review was conducted, searching for articles published from 1990 - 2012. The review found that nurse practitioners are key to the modernization of the National Health Service. Studies have shown that compared with doctors, nurse practitioners can be efficient and cost-effective in consultations. Qualitative research design. The information processing theory and think aloud approach were used to understand the cognitive processes of 10 participants (5 doctors and 5 nurse practitioners). One nurse practitioner was paired with one doctor from the same speciality and they were compared using a structured scenario-based interview. To ensure that all critical and relevant cues were covered by the individual participating in the scenario, a reference model was used to measure the degree of successful diagnosis, management and treatment. This study was conducted from May 2012 - January 2013. The data were processed for 5 months, from July to November 2012. The two groups of practitioners differed in the number of cue acquisitions obtained in the scenarios. In our study, nurse practitioners took 3 minutes longer to complete the scenarios. This study suggests that nurse practitioner consultations are comparable to those of medical doctors in a secondary care environment in terms of correct diagnoses and therapeutic treatments. The information processing theory highlighted that both groups of professionals had similar models for decision-making processes. © 2016 John Wiley & Sons Ltd.

Secondary flow structures in a 180∘ elastic curved vessel with torsion under steady and pulsatile inflow conditions

NASA Astrophysics Data System (ADS)

Najjari, Mohammad Reza; Plesniak, Michael W.

2017-11-01

Secondary flow vortical structures were investigated in an elastic 180° curved pipe with and without torsion under steady and pulsatile flow using particle image velocimetry (PIV). The elastic thin-walled curved pipes were constructed using Sylgard 184, and inserted into a bath of refractive index matched fluid to perform PIV. A vortex identification method was employed to identify various vortical structures in the flow. The secondary flow structures in the planar compliant model with dilatation of 0.61%-3.23% under pulsatile flow rate were compared with the rigid vessel model results, and it was found that local vessel compliance has a negligible effect on secondary flow morphology. The secondary flow structures were found to be more sensitive to out of plane curvature (torsion) than to vessel compliance. Torsion distorts the symmetry of secondary flow and results in more complex vortical structures in both steady and pulsatile flows. In high Re number steady flow with torsion, a single dominant vortical structure can be detected at the middle of the 90° cross section. In pulsatile flow with torsion, the split-Dean and Lyne-type vortices with same rotation direction originating from opposite sides of the cross section tend to merge together. supported by GW Center for Biomimetics and Bioinspired Engineering.

Population characteristics of submicrometer-sized craters on regolith particles from asteroid Itokawa

NASA Astrophysics Data System (ADS)

Matsumoto, Toru; Hasegawa, S.; Nakao, S.; Sakai, M.; Yurimoto, H.

2018-03-01

We investigated impact crater structures on regolith particles from asteroid Itokawa using scanning electron microscopy. We observed the surfaces of 51 Itokawa particles, ranging from 15 μm to 240 μm in size. Craters with average diameters ranging from 10 nm to 2.8 μm were identified on 13 Itokawa particles larger than 80 μm. We examined the abundance, spatial distribution, and morphology of approximately 900 craters on six Itokawa particles. Craters with sizes in excess of 200 nm are widely dispersed, with spatial densities from 2.6 μm2 to 4.5 μm2; a fraction of the craters was locally concentrated with a density of 0.1 μm2. The fractal dimension of the cumulative crater diameters ranges from 1.3 to 2.3. Craters of several tens of nanometers in diameter exhibit pit and surrounding rim structures. Craters of more than 100 nm in diameter commonly have melted residue at their bottom. These morphologies are similar to those of submicrometer-sized craters on lunar regolith. We estimated the impactor flux on Itokawa regolith-forming craters, assuming that the craters were accumulated during direct exposure to the space environment for 102 to 104 yr. The range of impactor flux onto Itokawa particles is estimated to be at least one order of magnitude higher than the interplanetary dust flux and comparable to the secondary impact flux on the Moon. This indicates that secondary ejecta impacts are probably the dominant cratering process in the submicrometer range on Itokawa regolith particles, as well as on the lunar surface. We demonstrate that secondary submicrometer craters can be produced anywhere in centimeter- to meter-sized depressions on Itokawa's surface through primary interplanetary dust impacts. If the surface unevenness on centimeter to meter scales is a significant factor determining the abundance of submicrometer secondary cratering, the secondary impact flux could be independent of the overall shapes or sizes of celestial bodies, and the secondary impact flux could have similar values on Itokawa and the Moon.

Mass spectrometric study of the negative and positive secondary ions emitted from ethanol microdroplets by MeV-energy heavy ion impact

NASA Astrophysics Data System (ADS)

Kitajima, Kensei; Majima, Takuya; Nishio, Tatsuya; Oonishi, Yoshiki; Mizutani, Shiori; Kohno, Jun-ya; Saito, Manabu; Tsuchida, Hidetsugu

2018-06-01

We have investigated the negative and positive secondary ions emitted from ethanol droplets by 4.0-MeV C3+ impact to reveal the characteristic features of the reaction processes induced by fast heavy ions at the liquid ethanol surface. Analysis of the secondary ions was performed by time-of-flight mass spectrometry for microdroplet targets in a high vacuum environment. Fragment ions, deprotonated cluster ions, and trace amounts of the reaction product ions are observed in the negative secondary ions. The main fragment anions are C2HmO- (m = 1, 3, and 5) and C2H- generated by loss of hydrogen and oxygen atoms. The reaction product anions include deprotonated glycols, larger alcohols, and their dehydrated and dehydrogenated forms generated by secondary reactions between fragments and radicals. Furthermore, C3Hm- (m = 0-2) and C4Hm- (m = 0 and 1) are observed, which could be produced through a plasma state generated in the heavy ion track. Deprotonated ethanol cluster ions, [(EtOH)n - H]-, are observed up to about n = 25. [(EtOH)n - H]- have smaller kinetic energies than the protonated cluster ions (EtOH)nH+. This probably represents the effect of the positive Coulomb potential transiently formed in the ion track. We also discuss the size distributions and structures of the water- and CH2OH-radical-attached ethanol cluster ions.

A parallel strategy for predicting the secondary structure of polycistronic microRNAs.

PubMed

Han, Dianwei; Tang, Guiliang; Zhang, Jun

2013-01-01

The biogenesis of a functional microRNA is largely dependent on the secondary structure of the microRNA precursor (pre-miRNA). Recently, it has been shown that microRNAs are present in the genome as the form of polycistronic transcriptional units in plants and animals. It will be important to design efficient computational methods to predict such structures for microRNA discovery and its applications in gene silencing. In this paper, we propose a parallel algorithm based on the master-slave architecture to predict the secondary structure from an input sequence. We conducted some experiments to verify the effectiveness of our parallel algorithm. The experimental results show that our algorithm is able to produce the optimal secondary structure of polycistronic microRNAs.

Peer Assessment among Secondary School Students: Introducing a Peer Feedback Tool in the Context of a Computer Supported Inquiry Learning Environment in Science

ERIC Educational Resources Information Center

Tsivitanidou, Olia; Zacharia, Zacharias C.; Hovardas, Tasos; Nicolaou, Aphrodite

2012-01-01

In this study we introduced a peer feedback tool to secondary school students while aiming at investigating whether this tool leads to a feedback dialogue when using a computer supported inquiry learning environment in science. Moreover, we aimed at examining what type of feedback students ask for and receive and whether the students use the…

Predicting the Attitudes and Self-Esteem of the Grade 9th Lower Secondary School Students towards Mathematics from Their Perceptions of the Classroom Learning Environment

ERIC Educational Resources Information Center

Tran, Van Dat

2012-01-01

This study reports the validity of the hypothesis that students' perceptions of the learning environment of mathematics classroom may predict their attitudes and self-esteem towards mathematics. It examines data from 487 grade 9th students from 14 mathematics classes in 7 Vietnamese lower secondary schools to identify how students' perceptions of…

Using FLUKA to Calculate Spacecraft: Single Event Environments: A Practical Approach

NASA Technical Reports Server (NTRS)

Koontz, Steve; Boeder, Paul; Reddell, Brandon

2009-01-01

The FLUKA nuclear transport and reaction code can be developed into a practical tool for calculation of spacecraft and planetary surface asset SEE and TID environments. Nuclear reactions and secondary particle shower effects can be estimated with acceptable accuracy both in-flight and in test. More detailed electronic device and/or spacecraft geometries than are reported here are possible using standard FLUKA geometry utilities. Spacecraft structure and shielding mass. Effects of high Z elements in microelectronic structure as reported previously. Median shielding mass in a generic slab or concentric sphere target geometry are at least approximately applicable to more complex spacecraft shapes. Need the spacecraft shielding mass distribution function applicable to the microelectronic system of interest. SEE environment effects can be calculated for a wide range of spacecraft and microelectronic materials with complete nuclear physics. Evaluate benefits of low Z shielding mass can be evaluated relative to aluminum. Evaluate effects of high Z elements as constituents of microelectronic devices. The principal limitation on the accuracy of the FLUKA based method reported here are found in the limited accuracy and incomplete character of affordable heavy ion test data. To support accurate rate estimates with any calculation method, the aspect ratio of the sensitive volume(s) and the dependence must be better characterized.

Deciphering the toxicity of bisphenol a to Candida rugosa lipase through spectrophotometric methods.

PubMed

Zhang, Rui; Zhao, Lining; Liu, Rutao

2016-10-01

Bisphenol A is widely used in the manufacture of food packaging and beverage containers and can invade our food and cause contamination. Candida rugose lipase has been a versatile enzyme for biocatalysis and biotransformations to produce useful materials for food, pharmaceutical and flavor. The interactions between bisphenol A and Candida rugosa lipase in vitro were studied by UV-vis, steady-state fluorescence, circular dichroism, synchronous fluorescence, light scattering spectra, molecular docking and enzyme activity assay to better understand the toxicity and toxic mechanisms of bisphenol A. The intrinsic fluorescence of the tryptophan amino acid residue and the secondary structure of the globular protein candida rugose lipase were made use of to thoroughly investigate the structural changes caused by bisphenol A. The results of the fluorescence indicated that bisphenol A interacted with candida rugose lipase and made tryptophan be exposed to a hydrophobic environment. Multi-spectroscopic measurements showed that the addition of bisphenol A increased the intrinsic fluorescence of Candida rugosa lipase, loosened its skeleton structure and changed its secondary structure. Also, the increased activity of Candida rugosa lipase revealed that the position or the structure of the catalytic triad of Candida rugosa lipase may be changed. The molecular docking results showed that bisphenol A bound with the residue Serine 209 which could be another reason for the increased activity of Candida rugosa lipase. Moreover, as can be seen from the results of resonance light scattering and dynamic light scattering, the volume of the Candida rugosa lipase was decreased and the lid may be stripped. Copyright © 2016 Elsevier B.V. All rights reserved.

The Globular State of the Single-Stranded RNA: Effect of the Secondary Structure Rearrangements

PubMed Central

Grigoryan, Zareh A.; Karapetian, Armen T.

2015-01-01

The mutual influence of the slow rearrangements of secondary structure and fast collapse of the long single-stranded RNA (ssRNA) in approximation of coarse-grained model is studied with analytic calculations. It is assumed that the characteristic time of the secondary structure rearrangement is much longer than that for the formation of the tertiary structure. A nonequilibrium phase transition of the 2nd order has been observed. PMID:26345143

Principles for Predicting RNA Secondary Structure Design Difficulty.

PubMed

Anderson-Lee, Jeff; Fisker, Eli; Kosaraju, Vineet; Wu, Michelle; Kong, Justin; Lee, Jeehyung; Lee, Minjae; Zada, Mathew; Treuille, Adrien; Das, Rhiju

2016-02-27

Designing RNAs that form specific secondary structures is enabling better understanding and control of living systems through RNA-guided silencing, genome editing and protein organization. Little is known, however, about which RNA secondary structures might be tractable for downstream sequence design, increasing the time and expense of design efforts due to inefficient secondary structure choices. Here, we present insights into specific structural features that increase the difficulty of finding sequences that fold into a target RNA secondary structure, summarizing the design efforts of tens of thousands of human participants and three automated algorithms (RNAInverse, INFO-RNA and RNA-SSD) in the Eterna massive open laboratory. Subsequent tests through three independent RNA design algorithms (NUPACK, DSS-Opt and MODENA) confirmed the hypothesized importance of several features in determining design difficulty, including sequence length, mean stem length, symmetry and specific difficult-to-design motifs such as zigzags. Based on these results, we have compiled an Eterna100 benchmark of 100 secondary structure design challenges that span a large range in design difficulty to help test future efforts. Our in silico results suggest new routes for improving computational RNA design methods and for extending these insights to assess "designability" of single RNA structures, as well as of switches for in vitro and in vivo applications. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Determination of secondary flow morphologies by wavelet analysis in a curved artery model with physiological inflow

NASA Astrophysics Data System (ADS)

Bulusu, Kartik V.; Hussain, Shadman; Plesniak, Michael W.

2014-11-01

Secondary flow vortical patterns in arterial curvatures have the potential to affect several cardiovascular phenomena, e.g., progression of atherosclerosis by altering wall shear stresses, carotid atheromatous disease, thoracic aortic aneurysms and Marfan's syndrome. Temporal characteristics of secondary flow structures vis-à-vis physiological (pulsatile) inflow waveform were explored by continuous wavelet transform (CWT) analysis of phase-locked, two-component, two-dimensional particle image velocimeter data. Measurements were made in a 180° curved artery test section upstream of the curvature and at the 90° cross-sectional plane. Streamwise, upstream flow rate measurements were analyzed using a one-dimensional antisymmetric wavelet. Cross-stream measurements at the 90° location of the curved artery revealed interesting multi-scale, multi-strength coherent secondary flow structures. An automated process for coherent structure detection and vortical feature quantification was applied to large ensembles of PIV data. Metrics such as the number of secondary flow structures, their sizes and strengths were generated at every discrete time instance of the physiological inflow waveform. An autonomous data post-processing method incorporating two-dimensional CWT for coherent structure detection was implemented. Loss of coherence in secondary flow structures during the systolic deceleration phase is observed in accordance with previous research. The algorithmic approach presented herein further elucidated the sensitivity and dependence of morphological changes in secondary flow structures on quasiperiodicity and magnitude of temporal gradients in physiological inflow conditions.

How Membrane-Active Peptides Get into Lipid Membranes.

PubMed

Sani, Marc-Antoine; Separovic, Frances

2016-06-21

The structure-function relationship for a family of antimicrobial peptides (AMPs) from the skin of Australian tree frogs is discussed and compared with that of peptide toxins from bee and Australian scorpion venoms. Although these membrane-active peptides induce a similar cellular fate by disrupting the lipid bilayer integrity, their lytic activity is achieved via different modes of action, which are investigated in relation to amino acid sequence, secondary structure, and membrane lipid composition. In order to better understand what structural features govern the interaction between peptides and lipid membranes, cell-penetrating peptides (CPPs), which translocate through the membrane without compromising its integrity, are also discussed. AMPs possess membrane lytic activities that are naturally designed to target the cellular membrane of pathogens or competitors. They are extremely diverse in amino acid composition and often show specificity against a particular strain of microbe. Since our antibiotic arsenal is declining precariously in the face of the rise in multiantibiotic resistance, AMPs increasingly are seen as a promising alternative. In an effort to understand their molecular mechanism, biophysical studies of a myriad of AMPs have been reported, yet no unifying mechanism has emerged, rendering difficult the rational design of drug leads. Similarly, a wide variety of cytotoxic peptides are found in venoms, the best known being melittin, yet again, predicting their activity based on a particular amino acid composition or secondary structure remains elusive. A common feature of these membrane-active peptides is their preference for the lipid environment. Indeed, they are mainly unstructured in solution and, in the presence of lipid membranes, quickly adsorb onto the surface, change their secondary structure, eventually insert into the hydrophobic core of the membrane bilayer, and finally disrupt the bilayer integrity. These steps define the molecular mechanism by which these membrane-active peptides lyse membranes. The last class of membrane-active peptides discussed are the CPPs, which translocate across the lipid bilayer without inducing severe disruption and have potential as drug vehicles. CPPs are typically highly charged and can show antimicrobial activity by targeting an intracellular target rather than via a direct membrane lytic mechanism. A critical aspect in the structure-function relationship of membrane-active peptides is their specific activity relative to the lipid membrane composition of the cell target. Cell membranes have a wide diversity of lipids, and those of eukaryotic and prokaryotic species differ greatly in composition and structure. The activity of AMPs from Australian tree frogs, toxins, and CPPs has been investigated within various lipid systems to assess whether a relationship between peptide and membrane composition could be identified. NMR spectroscopy techniques are being used to gain atomistic details of how these membrane-active peptides interact with model membranes and cells, and in particular, competitive assays demonstrate the difference between affinity and activity for a specific lipid environment. Overall, the interactions between these relatively small sized peptides and various lipid bilayers give insight into how these peptides function at the membrane interface.

Hot spot of structural ambivalence in prion protein revealed by secondary structure principal component analysis.

PubMed

Yamamoto, Norifumi

2014-08-21

The conformational conversion of proteins into an aggregation-prone form is a common feature of various neurodegenerative disorders including Alzheimer's, Huntington's, Parkinson's, and prion diseases. In the early stage of prion diseases, secondary structure conversion in prion protein (PrP) causing β-sheet expansion facilitates the formation of a pathogenic isoform with a high content of β-sheets and strong aggregation tendency to form amyloid fibrils. Herein, we propose a straightforward method to extract essential information regarding the secondary structure conversion of proteins from molecular simulations, named secondary structure principal component analysis (SSPCA). The definite existence of a PrP isoform with an increased β-sheet structure was confirmed in a free-energy landscape constructed by mapping protein structural data into a reduced space according to the principal components determined by the SSPCA. We suggest a "spot" of structural ambivalence in PrP-the C-terminal part of helix 2-that lacks a strong intrinsic secondary structure, thus promoting a partial α-helix-to-β-sheet conversion. This result is important to understand how the pathogenic conformational conversion of PrP is initiated in prion diseases. The SSPCA has great potential to solve various challenges in studying highly flexible molecular systems, such as intrinsically disordered proteins, structurally ambivalent peptides, and chameleon sequences.

Computational analysis of conserved RNA secondary structure in transcriptomes and genomes.

PubMed

Eddy, Sean R

2014-01-01

Transcriptomics experiments and computational predictions both enable systematic discovery of new functional RNAs. However, many putative noncoding transcripts arise instead from artifacts and biological noise, and current computational prediction methods have high false positive rates. I discuss prospects for improving computational methods for analyzing and identifying functional RNAs, with a focus on detecting signatures of conserved RNA secondary structure. An interesting new front is the application of chemical and enzymatic experiments that probe RNA structure on a transcriptome-wide scale. I review several proposed approaches for incorporating structure probing data into the computational prediction of RNA secondary structure. Using probabilistic inference formalisms, I show how all these approaches can be unified in a well-principled framework, which in turn allows RNA probing data to be easily integrated into a wide range of analyses that depend on RNA secondary structure inference. Such analyses include homology search and genome-wide detection of new structural RNAs.

PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction

PubMed Central

Harmanci, Arif Ozgun; Sharma, Gaurav; Mathews, David H.

2008-01-01

A novel method is presented for joint prediction of alignment and common secondary structures of two RNA sequences. The joint consideration of common secondary structures and alignment is accomplished by structural alignment over a search space defined by the newly introduced motif called matched helical regions. The matched helical region formulation generalizes previously employed constraints for structural alignment and thereby better accommodates the structural variability within RNA families. A probabilistic model based on pseudo free energies obtained from precomputed base pairing and alignment probabilities is utilized for scoring structural alignments. Maximum a posteriori (MAP) common secondary structures, sequence alignment and joint posterior probabilities of base pairing are obtained from the model via a dynamic programming algorithm called PARTS. The advantage of the more general structural alignment of PARTS is seen in secondary structure predictions for the RNase P family. For this family, the PARTS MAP predictions of secondary structures and alignment perform significantly better than prior methods that utilize a more restrictive structural alignment model. For the tRNA and 5S rRNA families, the richer structural alignment model of PARTS does not offer a benefit and the method therefore performs comparably with existing alternatives. For all RNA families studied, the posterior probability estimates obtained from PARTS offer an improvement over posterior probability estimates from a single sequence prediction. When considering the base pairings predicted over a threshold value of confidence, the combination of sensitivity and positive predictive value is superior for PARTS than for the single sequence prediction. PARTS source code is available for download under the GNU public license at http://rna.urmc.rochester.edu. PMID:18304945

Secondary Moments due to Prestressing with Different Bond at the Ultimate Limit State

NASA Astrophysics Data System (ADS)

Halvoník, Jaroslav; Pažma, Peter; Vida, Radoslav

2018-03-01

Secondary effects of prestressing develop in statically indeterminate structures (e.g., continuous beams) due to the restraint of deformations imposed by hyperstatic restraints. These effects may significantly influence internal forces and stresses in prestressed structures. Secondary effects are influenced by the redundancy of a structural system, which raises the question of whether they will remain constant after a change in the structural system, e.g., due to the development of plastic hinge(s) in a critical cross-section(s) or after the development of a kinematic mechanism, or if they will disappear when the structure changes into a sequence of simply supported beams. The paper deals with an investigation of the behavior of continuous post-tensioned beams subjected to an ultimate load with significant secondary effects from prestressing. A total of 6 two-span beams prestressed by tendons with different bonds were tested in a laboratory with a load that changed their structural system into a kinematic mechanism. The internal forces and secondary effects of the prestressing were controlled through measurements of the reactions in all the supports. The results revealed that the secondary effects remained as a permanent part of the action on the experimental beams, even after the development of the kinematic mechanism. The results obtained confirmed that secondary effects should be included in all combinations of actions for verifications of ultimate limit states (ULS).

[Changes in the secondary and tertiary structure of serum albumin in interactions with ligands of various structures].

PubMed

Trinus, F P; Braver-Chernobul'skaia, B S; Luĭk, A I; Boldeskul, A E; Velichko, A N

1984-01-01

High affinity interactions between blood serum albumin and five substances of various chemical structure, exhibiting distinct physiological activity, were accompanied by alterations in the protein tertiary structure, while the albumin secondary structure was involved in conformational transformation after less effective affinity binding.

School food policies and practices: a state-wide survey of secondary school principals.

PubMed

French, Simone A; Story, Mary; Fulkerson, Jayne A

2002-12-01

To describe food-related policies and practices in secondary schools in Minnesota. Mailed anonymous survey including questions about the secondary school food environment and food-related practices and policies. Members of a statewide professional organization for secondary school principals (n = 610; response rate: 463/610 = 75%). Of the 463 surveys returned, 336 met the eligibility criteria (current position was either principal or assistant principal and school included at least one of the grades of 9 through 12). Descriptive statistics examined the prevalence of specific policies and practices. Chi2 analysis examined associations between policies and practices and school variables. Among principals, 65% believed it was important to have a nutrition policy for the high school; however, only 32% reported a policy at their school. Principals reported positive attitudes about providing a healthful school food environment, but 98% of the schools had soft drink vending machines and 77% had contracts with soft drink companies. Food sold at school fundraisers was most often candy, fruit, and cookies. Dietetics professionals who work in secondary school settings should collaborate with other key school staff members and parents to develop and implement a comprehensive school nutrition policy. Such a policy could foster a school food environment that is supportive of healthful food choices among youth.

Antimicrobial properties and the influence of temperature on secondary metabolite production in cold environment soil fungi

NASA Astrophysics Data System (ADS)

Yogabaanu, U.; Weber, Jean-Frederic Faizal; Convey, Peter; Rizman-Idid, Mohammed; Alias, Siti Aisyah

2017-12-01

The Arctic and Antarctic share environmental extremes. To survive in such environments, microbes such as soil fungi need to compete with or protect themselves effectively from other soil microbiota and to obtain the often scarce nutrients available, and many use secondary metabolites to facilitate this. We therefore (i) screened for antimicrobial properties of cold-environment Arctic and Antarctic soil fungi, and (ii) identified changes in the secreted secondary metabolite profiles of a subset of these strains in response to temperature variation. A total of 40 polar soil fungal strains from King George Island, maritime Antarctic and Hornsund, Svalbard, High Arctic, were obtained from the Malaysian National Antarctic Research Centre culture collections. The plug assay technique was used to screen for antimicrobial potential against Gram-positive and Gram-negative human pathogenic bacteria (Bacillus subtilis, B. cereus, Pseudomonas aeruginosa, Enterococcus faecalis and Escherichia coli). About 45% of the tested fungal strains showed antimicrobial activity against at least one tested microorganism. Three fungal isolates showed good bioactivity and were subjected to secondary metabolite profiling at different temperatures (4, 10, 15 and 28 °C). We observed a range of responses in fungal metabolite production when incubated at varying temperatures, confirming an influence of environmental conditions such as temperature on the production of secondary metabolites.

Oil platforms off California are among the most productive marine fish habitats globally

PubMed Central

Claisse, Jeremy T.; Pondella, Daniel J.; Love, Milton; Zahn, Laurel A.; Williams, Chelsea M.; Williams, Jonathan P.; Bull, Ann S.

2014-01-01

Secondary (i.e., heterotrophic or animal) production is a main pathway of energy flow through an ecosystem as it makes energy available to consumers, including humans. Its estimation can play a valuable role in the examination of linkages between ecosystem functions and services. We found that oil and gas platforms off the coast of California have the highest secondary fish production per unit area of seafloor of any marine habitat that has been studied, about an order of magnitude higher than fish communities from other marine ecosystems. Most previous estimates have come from estuarine environments, generally regarded as one of the most productive ecosystems globally. High rates of fish production on these platforms ultimately result from high levels of recruitment and the subsequent growth of primarily rockfish (genus Sebastes) larvae and pelagic juveniles to the substantial amount of complex hardscape habitat created by the platform structure distributed throughout the water column. The platforms have a high ratio of structural surface area to seafloor surface area, resulting in large amounts of habitat for juvenile and adult demersal fishes over a relatively small footprint of seafloor. Understanding the biological implications of these structures will inform policy related to the decommissioning of existing (e.g., oil and gas platforms) and implementation of emerging (e.g., wind, marine hydrokinetic) energy technologies. PMID:25313050

Delipidation of Cytochrome c Oxidase from Rhodobacter sphaeroides Destabilizes its Quaternary Structure

PubMed Central

Musatov, Andrej; Varhač, Rastislav; Hosler, Jonathan P.; Sedlák, Erik

2016-01-01

Delipidation of detergent-solubilized cytochrome c oxidase isolated from Rhodobacter sphaeroides (Rbs-CcO) has no apparent structural and/or functional effect on the protein, however affects its resistance against thermal or chemical denaturation. Phospholipase A2 (PLA2) hydrolysis of phospholipids that are co-purified with the enzyme removes all but two tightly bound phosphatidylethanolamines. Replacement of the removed phospholipids with nonionic detergent decreases both thermal stability of the enzyme and its resilience against the effect of chemical denaturants such as urea. In contrast to nondelipidated Rbs-CcO, the enzymatic activity of PLA2-treated Rbs-CcO is substantially diminished after exposure to high (>4M) urea concentration at room temperature without an alteration of its secondary structure. Absorbance spectroscopy and sedimentation velocity experiments revealed a strong correlation between intact tertiary structure of heme regions and quaternary structure, respectively, and the enzymatic activity of the protein. We concluded that phospholipid environment of Rbs-CcO has the protective role for stability of its tertiary and quaternary structures. PMID:26923069

Structure-function relationship of reduced cytochrome c probed by complete solution structure determination in 30% acetonitrile/water solution.

PubMed

Sivakolundu, Sivashankar G; Mabrouk, Patricia Ann

2003-05-01

The complete solution structure of ferrocytochrome c in 30% acetonitrile/70% water has been determined using high-field 1D and 2D (1)H NMR methods and deposited in the Protein Data Bank with codes 1LC1 and 1LC2. This is the first time a complete solution protein structure has been determined for a protein in nonaqueous media. Ferrocyt c retains a native protein secondary structure (five alpha-helices and two omega loops) in 30% acetonitrile. H18 and M80 residues are the axial heme ligands, as in aqueous solution. Residues believed to be axial heme ligands in the alkaline-like conformers of ferricyt c, specifically H33 and K72, are positioned close to the heme iron. The orientations of both heme propionates are markedly different in 30% acetonitrile/70% water. Comparative structural analysis of reduced cyt c in 30% acetonitrile/70% water solution with cyt c in different environments has given new insight into the cyt c folding mechanism, the electron transfer pathway, and cell apoptosis.

Protein modeling and molecular dynamics simulation of SlWRKY4 protein cloned from drought tolerant tomato (Solanum habrochaites) line EC520061.

PubMed

Karkute, Suhas G; Easwaran, Murugesh; Gujjar, Ranjit Singh; Piramanayagam, Shanmughavel; Singh, Major

2015-10-01

WRKY genes are members of one of the largest families of plant transcription factors and play an important role in response to biotic and abiotic stresses, and overall growth and development. Understanding the interaction of WRKY proteins with other proteins/ligands in plant cells is of utmost importance to develop plants having tolerance to biotic and abiotic stresses. The SlWRKY4 gene was cloned from a drought tolerant wild species of tomato (Solanum habrochaites) and the secondary structure and 3D modeling of this protein were predicted using Schrödinger Suite-Prime. Predicted structures were also subjected to plot against Ramachandran's conformation, and the modeled structure was minimized using Macromodel. Finally, the minimized structure was simulated in the water environment to check the protein stability. The behavior of the modeled structure was well-simulated and analyzed through RMSD and RMSF of the protein. The present work provides the modeled 3D structure of SlWRKY4 that will help in understanding the mechanism of gene regulation by further in silico interaction studies.

Residue-residue contacts: application to analysis of secondary structure interactions.

PubMed

Potapov, Vladimir; Edelman, Marvin; Sobolev, Vladimir

2013-01-01

Protein structures and their complexes are formed and stabilized by interactions, both inside and outside of the protein. Analysis of such interactions helps in understanding different levels of structures (secondary, super-secondary, and oligomeric states). It can also assist molecular biologists in understanding structural consequences of modifying proteins and/or ligands. In this chapter, our definition of atom-atom and residue-residue contacts is described and applied to analysis of protein-protein interactions in dimeric β-sandwich proteins.

40 CFR 50.15 - National primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2013 CFR

2013-07-01

... air quality standards for ozone. 50.15 Section 50.15 Protection of Environment ENVIRONMENTAL....15 National primary and secondary ambient air quality standards for ozone. (a) The level of the national 8-hour primary and secondary ambient air quality standards for ozone (O3) is 0.075 parts per...

40 CFR 50.15 - National primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2012 CFR

2012-07-01

... air quality standards for ozone. 50.15 Section 50.15 Protection of Environment ENVIRONMENTAL....15 National primary and secondary ambient air quality standards for ozone. (a) The level of the national 8-hour primary and secondary ambient air quality standards for ozone (O3) is 0.075 parts per...

40 CFR 50.15 - National primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2014 CFR

2014-07-01

... air quality standards for ozone. 50.15 Section 50.15 Protection of Environment ENVIRONMENTAL....15 National primary and secondary ambient air quality standards for ozone. (a) The level of the national 8-hour primary and secondary ambient air quality standards for ozone (O3) is 0.075 parts per...

40 CFR 50.15 - National primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2011 CFR

2011-07-01

... air quality standards for ozone. 50.15 Section 50.15 Protection of Environment ENVIRONMENTAL....15 National primary and secondary ambient air quality standards for ozone. (a) The level of the national 8-hour primary and secondary ambient air quality standards for ozone (O3) is 0.075 parts per...

40 CFR 50.15 - National primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2010 CFR

2010-07-01

... air quality standards for ozone. 50.15 Section 50.15 Protection of Environment ENVIRONMENTAL....15 National primary and secondary ambient air quality standards for ozone. (a) The level of the national 8-hour primary and secondary ambient air quality standards for ozone (O3) is 0.075 parts per...

Energy Use and the Environment. Concepts & Activities for the Classroom: Secondary Social Studies Module.

ERIC Educational Resources Information Center

Hawaii State Dept. of Education, Honolulu. Office of Instructional Services.

As part of a comprehensive, interdisciplinary environmental education program for elementary and secondary education in Hawaii, this teaching guide provides a variety of energy education activities for secondary social studies. An extensive introduction outlines the total program and how it fits into the general education program. It explains how…

The Nature of Laboratory Learning Experiences in Secondary Science Online

ERIC Educational Resources Information Center

Crippen, Kent J.; Archambault, Leanna M.; Kern, Cindy L.

2013-01-01

Teaching science to secondary students in an online environment is a growing international trend. Despite this trend, reports of empirical studies of this phenomenon are noticeably missing. With a survey concerning the nature of laboratory activities, this study describes the perspective of 35-secondary teachers from 15-different U.S. states who…

40 CFR 143.3 - Secondary maximum contaminant levels.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false Secondary maximum contaminant levels... levels. The secondary maximum contaminant levels for public water systems are as follows: Contaminant Level Aluminum 0.05 to 0.2 mg/l. Chloride 250 mg/l. Color 15 color units. Copper 1.0 mg/l. Corrosivity...

40 CFR 50.16 - National primary and secondary ambient air quality standards for lead.

Code of Federal Regulations, 2011 CFR

2011-07-01

... air quality standards for lead. 50.16 Section 50.16 Protection of Environment ENVIRONMENTAL PROTECTION... National primary and secondary ambient air quality standards for lead. (a) The national primary and secondary ambient air quality standards for lead (Pb) and its compounds are 0.15 micrograms per cubic meter...

40 CFR 50.12 - National primary and secondary ambient air quality standards for lead.

Code of Federal Regulations, 2013 CFR

2013-07-01

... air quality standards for lead. 50.12 Section 50.12 Protection of Environment ENVIRONMENTAL PROTECTION... National primary and secondary ambient air quality standards for lead. (a) National primary and secondary ambient air quality standards for lead and its compounds, measured as elemental lead by a reference method...

40 CFR 50.12 - National primary and secondary ambient air quality standards for lead.

Code of Federal Regulations, 2012 CFR

2012-07-01

... air quality standards for lead. 50.12 Section 50.12 Protection of Environment ENVIRONMENTAL PROTECTION... National primary and secondary ambient air quality standards for lead. (a) National primary and secondary ambient air quality standards for lead and its compounds, measured as elemental lead by a reference method...

40 CFR 50.12 - National primary and secondary ambient air quality standards for lead.

Code of Federal Regulations, 2011 CFR

2011-07-01

... air quality standards for lead. 50.12 Section 50.12 Protection of Environment ENVIRONMENTAL PROTECTION... National primary and secondary ambient air quality standards for lead. (a) National primary and secondary ambient air quality standards for lead and its compounds, measured as elemental lead by a reference method...

Authentic leadership, organizational culture, and healthy work environments.

PubMed

Shirey, Maria R

2009-01-01

The purpose of this article is to showcase the relationship among authentic leadership, organizational culture, and healthy work environments using a stress and coping lens. A qualitative descriptive study was conducted to determine what situations contribute to nurse manager stress, what coping strategies they utilize, what health outcomes they report, and what decision-making processes they follow to address stressful situations in their roles. A purposive sample of 21 nurse managers employed at 3 US acute care hospitals completed a demographic questionnaire and 14-question interview incorporating components of the Critical Decision Method. A secondary analysis of the data was conducted to identify differences in nurse manager narratives based upon differences in the organizational cultures where the managers worked. Of the 21 nurse managers studied, differences were evident in the organizational cultures reported. Nurse managers working in the positive organizational cultures (n = 12) generally worked in healthy work environments and engaged in more authentic leadership behaviors. Conversely, nurse managers working in the negative organizational cultures (n = 9) worked in unhealthy work environments and reported less optimism and more challenges engaging in authentic leadership practices. Organizational culture and leadership matter in creating and sustaining healthy work environments. Nurse managers play a pivotal role in creating these environments, yet they need supportive structures and resources to more effectively execute their roles.

Polarization-dependent two-photon absorption for the determination of protein secondary structure: A theoretical study

NASA Astrophysics Data System (ADS)

Wanapun, Duangporn; Wampler, Ronald D.; Begue, Nathan J.; Simpson, Garth J.

2008-03-01

A new method for sensitive determination of protein secondary structure via multi-photon absorption is considered theoretically. Perturbation theory is developed to describe the polarization-dependent two-photon absorption (TPA) of α-helix and β-sheet protein secondary structures. The exciton coupling interactions responsible for relatively weak electronic circular dichroism in one-photon absorption are predicted to give rise to large changes in the TPA cross-section (>200%) for circular versus linear incident polarizations, defined as CLD. The CLD effect in TPA is electric dipole-allowed, which explains the much greater sensitivity. These predictions suggest TPA should be a viable means of sensitively probing protein secondary structure.

Accelerated stability studies for moisture-induced aggregation of tetanus toxoid.

PubMed

Jain, Nishant Kumar; Roy, Ipsita

2011-03-01

The study was carried out to evaluate the effect of exposing solid tetanus toxoid to moisture in two different ways on the structure and function of the toxoid. Tetanus toxoid was exposed to moisture by (i) the addition of an optimized amount of buffer and (ii) incubation under an environment provided by a saturated solution of K(2)CrO(4.) The changes in the conformational, structural and antigenic properties of tetanus toxoid were measured and compared. Results show that even at a similar level of moisture-induced aggregation, the amounts of water absorbed by the two preparations of tetanus toxoid are different. Differences in antigenicity and changes in structure of the toxoid at primary, secondary and tertiary structure levels were seen. Although both conditions are used to mimic accelerated stability conditions in the laboratory, the final products are different in the two cases. Thus, conditions for 'accelerated stability studies' for therapeutic proteins need to be selected with care so that they resemble the fate of the actual product.

High performance EUV multilayer structures insensitive to capping layer optical parameters.

PubMed

Pelizzo, Maria Guglielmina; Suman, Michele; Monaco, Gianni; Nicolosi, Piergiorgio; Windt, David L

2008-09-15

We have designed and tested a-periodic multilayer structures containing protective capping layers in order to obtain improved stability with respect to any possible changes of the capping layer optical properties (due to oxidation and contamination, for example)-while simultaneously maximizing the EUV reflection efficiency for specific applications, and in particular for EUV lithography. Such coatings may be particularly useful in EUV lithographic apparatus, because they provide both high integrated photon flux and higher stability to the harsh operating environment, which can affect seriously the performance of the multilayer-coated projector system optics. In this work, an evolutive algorithm has been developed in order to design these a-periodic structures, which have been proven to have also the property of stable performance with respect to random layer thickness errors that might occur during coating deposition. Prototypes have been fabricated, and tested with EUV and X-ray reflectometry, and secondary electron spectroscopy. The experimental results clearly show improved performance of our new a-periodic coatings design compared with standard periodic multilayer structures.

Multiscale integral analysis of a HT leakage in a fusion nuclear power plant

NASA Astrophysics Data System (ADS)

Velarde, M.; Fradera, J.; Perlado, J. M.; Zamora, I.; Martínez-Saban, E.; Colomer, C.; Briani, P.

2016-05-01

The present work presents an example of the application of an integral methodology based on a multiscale analysis that covers the whole tritium cycle within a nuclear fusion power plant, from a micro scale, analyzing key components where tritium is leaked through permeation, to a macro scale, considering its atmospheric transport. A leakage from the Nuclear Power Plants, (NPP) primary to the secondary side of a heat exchanger (HEX) is considered for the present example. Both primary and secondary loop coolants are assumed to be He. Leakage is placed inside the HEX, leaking tritium in elementary tritium (HT) form to the secondary loop where it permeates through the piping structural material to the exterior. The Heating Ventilation and Air Conditioning (HVAC) system removes the leaked tritium towards the NPP exhaust. The HEX is modelled with system codes and coupled to Computational Fluid Dynamic (CFD) to account for tritium dispersion inside the nuclear power plants buildings and in site environment. Finally, tritium dispersion is calculated with an atmospheric transport code and a dosimetry analysis is carried out. Results show how the implemented methodology is capable of assessing the impact of tritium from the microscale to the atmospheric scale including the dosimetric aspect.

Metal-assisted SIMS and cluster ion bombardment for ion yield enhancement

NASA Astrophysics Data System (ADS)

Heile, A.; Lipinsky, D.; Wehbe, N.; Delcorte, A.; Bertrand, P.; Felten, A.; Houssiau, L.; Pireaux, J.-J.; De Mondt, R.; Van Vaeck, L.; Arlinghaus, H. F.

2008-12-01

In addition to structural information, a detailed knowledge of the local chemical environment proves to be of ever greater importance, for example for the development of new types of materials as well as for specific modifications of surfaces and interfaces in multiple fields of materials science or various biomedical and chemical applications. But the ongoing miniaturization and therefore reduction of the amount of material available for analysis constitute a challenge to the detection limits of analytical methods. In the case of time-of-flight secondary ion mass spectrometry (TOF-SIMS), several methods of secondary ion yield enhancement have been proposed. This paper focuses on the investigation of the effects of two of these methods, metal-assisted SIMS and polyatomic primary ion bombardment. For this purpose, thicker layers of polystyrene (PS), both pristine and metallized with different amounts of gold, were analyzed using monoatomic (Ar +, Ga +, Xe +, Bi +) and polyatomic (SF 5+, Bi 3+, C 60+) primary ions. It was found that polyatomic ions generally induce a significant increase of the secondary ion yield. On the other hand, with gold deposition, a yield enhancement can only be detected for monoatomic ion bombardment.

DNA secondary structures: stability and function of G-quadruplex structures

PubMed Central

Bochman, Matthew L.; Paeschke, Katrin; Zakian, Virginia A.

2013-01-01

In addition to the canonical double helix, DNA can fold into various other inter- and intramolecular secondary structures. Although many such structures were long thought to be in vitro artefacts, bioinformatics demonstrates that DNA sequences capable of forming these structures are conserved throughout evolution, suggesting the existence of non-B-form DNA in vivo. In addition, genes whose products promote formation or resolution of these structures are found in diverse organisms, and a growing body of work suggests that the resolution of DNA secondary structures is critical for genome integrity. This Review focuses on emerging evidence relating to the characteristics of G-quadruplex structures and the possible influence of such structures on genomic stability and cellular processes, such as transcription. PMID:23032257

Bioinformatics approaches for structural and functional analysis of proteins in secondary metabolism in Withania somnifera.

PubMed

Sanchita; Singh, Swati; Sharma, Ashok

2014-11-01

Withania somnifera (Ashwagandha) is an affluent storehouse of large number of pharmacologically active secondary metabolites known as withanolides. These secondary metabolites are produced by withanolide biosynthetic pathway. Very less information is available on structural and functional aspects of enzymes involved in withanolides biosynthetic pathways of Withiana somnifera. We therefore performed a bioinformatics analysis to look at functional and structural properties of these important enzymes. The pathway enzymes taken for this study were 3-Hydroxy-3-methylglutaryl coenzyme A reductase, 1-Deoxy-D-xylulose-5-phosphate synthase, 1-Deoxy-D-xylulose-5-phosphate reductase, farnesyl pyrophosphate synthase, squalene synthase, squalene epoxidase, and cycloartenol synthase. The prediction of secondary structure was performed for basic structural information. Three-dimensional structures for these enzymes were predicted. The physico-chemical properties such as pI, AI, GRAVY and instability index were also studied. The current information will provide a platform to know the structural attributes responsible for the function of these protein until experimental structures become available.

DSSPcont: continuous secondary structure assignments for proteins

PubMed Central

Carter, Phil; Andersen, Claus A. F.; Rost, Burkhard

2003-01-01

The DSSP program automatically assigns the secondary structure for each residue from the three-dimensional co-ordinates of a protein structure to one of eight states. However, discrete assignments are incomplete in that they cannot capture the continuum of thermal fluctuations. Therefore, DSSPcont (http://cubic.bioc.columbia.edu/services/DSSPcont) introduces a continuous assignment of secondary structure that replaces ‘static’ by ‘dynamic’ states. Technically, the continuum results from calculating weighted averages over 10 discrete DSSP assignments with different hydrogen bond thresholds. A DSSPcont assignment for a particular residue is a percentage likelihood of eight secondary structure states, derived from a weighted average of the ten DSSP assignments. The continuous assignments have two important features: (i) they reflect the structural variations due to thermal fluctuations as detected by NMR spectroscopy; and (ii) they reproduce the structural variation between many NMR models from one single model. Therefore, functionally important variation can be extracted from a single X-ray structure using the continuous assignment procedure. PMID:12824310

Observation and analysis of emergent coherent structures in a high-energy-density shock-driven planar mixing layer experiment

DOE PAGES

Doss, Forrest William; Flippo, Kirk Adler; Merritt, Elizabeth Catherine

2016-08-03

Coherent emergent structures have been observed in a high-energy-density supersonic mixing layer experiment. A millimeter-scale shock tube uses lasers to drive Mbar shocks into the tube volume. The shocks are driven into initially solid foam (60 mg/cm 3) hemicylinders separated by an Al or Ti metal tracer strip; the components are vaporized by the drive. Before the experiment disassembles, the shocks cross at the tube center, creating a very fast (ΔU > 200 km/s) shear-unstable zone. After several nanoseconds, an expanding mixing layer is measured, and after 10+ ns we observe the appearance of streamwise-periodic, spanwise-aligned rollers associated with themore » primary Kelvin-Helmholtz instability of mixing layers. We additionally image roller pairing and spanwise-periodic streamwise-aligned filaments associated with secondary instabilities. New closures are derived to connect length scales of these structures to estimates of fluctuating velocity data otherwise unobtainable in the high-energy-density environment. Finally, this analysis indicates shear-induced specific turbulent energies 10 3 – 10 4 times higher than the nearest conventional experiments. Because of difficulties in continuously driving systems under these conditions and the harshness of the experimental environment limiting the usable diagnostics, clear evidence of these developing structures has never before been observed in this regime.« less

Student Perceptions of Chemistry Laboratory Learning Environments, Student-Teacher Interactions and Attitudes in Secondary School Gifted Education Classes in Singapore

NASA Astrophysics Data System (ADS)

Lang, Quek Choon; Wong, Angela F. L.; Fraser, Barry J.

2005-09-01

This study investigated the chemistry laboratory classroom environment, teacher-student interactions and student attitudes towards chemistry among 497 gifted and non-gifted secondary-school students in Singapore. The data were collected using the 35-item Chemistry Laboratory Environment Inventory (CLEI), the 48-item Questionnaire on Teacher Interaction (QTI) and the 30-item Questionnaire on Chemistry-Related Attitudes (QOCRA). Results supported the validity and reliability of the CLEI and QTI for this sample. Stream (gifted versus non-gifted) and gender differences were found in actual and preferred chemistry laboratory classroom environments and teacher-student interactions. Some statistically significant associations of modest magnitude were found between students' attitudes towards chemistry and both the laboratory classroom environment and the interpersonal behaviour of chemistry teachers. Suggestions for improving chemistry laboratory classroom environments and the teacher-student interactions for gifted students are provided.

RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure.

PubMed

Liu, Qi; Yang, Yu; Chen, Chun; Bu, Jiajun; Zhang, Yin; Ye, Xiuzi

2008-03-31

With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression. RNACompress employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1) present a robust and effective way for RNA structural data compression; (2) design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that RNACompress achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as Gencompress, winrar and gzip. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers) compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective. A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed RNACompress, as a useful tool for academic users. Extensive tests have shown that RNACompress is a universally efficient algorithm for the compression of RNA sequences with their secondary structures. RNACompress also serves as a good measurement of the informational complexity of RNA secondary structure, which can be used to study the functional activities of RNA molecules.

RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure

PubMed Central

Liu, Qi; Yang, Yu; Chen, Chun; Bu, Jiajun; Zhang, Yin; Ye, Xiuzi

2008-01-01

Background With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression. Results RNACompress employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1) present a robust and effective way for RNA structural data compression; (2) design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that RNACompress achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as Gencompress, winrar and gzip. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers) compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective. Conclusion A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed RNACompress, as a useful tool for academic users. Extensive tests have shown that RNACompress is a universally efficient algorithm for the compression of RNA sequences with their secondary structures. RNACompress also serves as a good measurement of the informational complexity of RNA secondary structure, which can be used to study the functional activities of RNA molecules. PMID:18373878

Robust prediction of consensus secondary structures using averaged base pairing probability matrices.

PubMed

Kiryu, Hisanori; Kin, Taishin; Asai, Kiyoshi

2007-02-15

Recent transcriptomic studies have revealed the existence of a considerable number of non-protein-coding RNA transcripts in higher eukaryotic cells. To investigate the functional roles of these transcripts, it is of great interest to find conserved secondary structures from multiple alignments on a genomic scale. Since multiple alignments are often created using alignment programs that neglect the special conservation patterns of RNA secondary structures for computational efficiency, alignment failures can cause potential risks of overlooking conserved stem structures. We investigated the dependence of the accuracy of secondary structure prediction on the quality of alignments. We compared three algorithms that maximize the expected accuracy of secondary structures as well as other frequently used algorithms. We found that one of our algorithms, called McCaskill-MEA, was more robust against alignment failures than others. The McCaskill-MEA method first computes the base pairing probability matrices for all the sequences in the alignment and then obtains the base pairing probability matrix of the alignment by averaging over these matrices. The consensus secondary structure is predicted from this matrix such that the expected accuracy of the prediction is maximized. We show that the McCaskill-MEA method performs better than other methods, particularly when the alignment quality is low and when the alignment consists of many sequences. Our model has a parameter that controls the sensitivity and specificity of predictions. We discussed the uses of that parameter for multi-step screening procedures to search for conserved secondary structures and for assigning confidence values to the predicted base pairs. The C++ source code that implements the McCaskill-MEA algorithm and the test dataset used in this paper are available at http://www.ncrna.org/papers/McCaskillMEA/. Supplementary data are available at Bioinformatics online.

Secondary flow vortical structures in a 180∘ elastic curved vessel with torsion under steady and pulsatile inflow conditions

NASA Astrophysics Data System (ADS)

Najjari, Mohammad Reza; Plesniak, Michael W.

2018-01-01

Secondary flow structures in a 180∘ curved pipe model of an artery are studied using particle image velocimetry. Both steady and pulsatile inflow conditions are investigated. In planar curved pipes with steady flow, multiple (two, four, six) vortices are detected. For pulsatile flow, various pairs of vortices, i.e., Dean, deformed-Dean, Lyne-type, and split-Dean, are present in the cross section of the pipe at 90∘ into the bend. The effects of nonplanar curvature (torsion) and vessel dilatation on these vortical structures are studied. Torsion distorts the symmetric secondary flows (which exist in planar curvatures) and can result in formation of more complex vortical structures. For example, the split-Dean and Lyne-type vortices with same rotation direction originating from opposite sides of the cross section tend to merge together in pulsatile flow. The vortical structures in elastic vessels with dilatation (0.61%-3.23%) are also investigated and the results are compared with rigid model results. It was found that the secondary flow structures in rigid and elastic models are similar, and hence the local compliance of the vessel does not affect the morphology of secondary flow structures.

RNAmutants: a web server to explore the mutational landscape of RNA secondary structures

PubMed Central

Waldispühl, Jerome; Devadas, Srinivas; Berger, Bonnie; Clote, Peter

2009-01-01

The history and mechanism of molecular evolution in DNA have been greatly elucidated by contributions from genetics, probability theory and bioinformatics—indeed, mathematical developments such as Kimura's neutral theory, Kingman's coalescent theory and efficient software such as BLAST, ClustalW, Phylip, etc., provide the foundation for modern population genetics. In contrast to DNA, the function of most noncoding RNA depends on tertiary structure, experimentally known to be largely determined by secondary structure, for which dynamic programming can efficiently compute the minimum free energy secondary structure. For this reason, understanding the effect of pointwise mutations in RNA secondary structure could reveal fundamental properties of structural RNA molecules and improve our understanding of molecular evolution of RNA. The web server RNAmutants provides several efficient tools to compute the ensemble of low-energy secondary structures for all k-mutants of a given RNA sequence, where k is bounded by a user-specified upper bound. As we have previously shown, these tools can be used to predict putative deleterious mutations and to analyze regulatory sequences from the hepatitis C and human immunodeficiency genomes. Web server is available at http://bioinformatics.bc.edu/clotelab/RNAmutants/, and downloadable binaries at http://rnamutants.csail.mit.edu/. PMID:19531740

Ensemble-based prediction of RNA secondary structures.

PubMed

Aghaeepour, Nima; Hoos, Holger H

2013-04-24

Accurate structure prediction methods play an important role for the understanding of RNA function. Energy-based, pseudoknot-free secondary structure prediction is one of the most widely used and versatile approaches, and improved methods for this task have received much attention over the past five years. Despite the impressive progress that as been achieved in this area, existing evaluations of the prediction accuracy achieved by various algorithms do not provide a comprehensive, statistically sound assessment. Furthermore, while there is increasing evidence that no prediction algorithm consistently outperforms all others, no work has been done to exploit the complementary strengths of multiple approaches. In this work, we present two contributions to the area of RNA secondary structure prediction. Firstly, we use state-of-the-art, resampling-based statistical methods together with a previously published and increasingly widely used dataset of high-quality RNA structures to conduct a comprehensive evaluation of existing RNA secondary structure prediction procedures. The results from this evaluation clarify the performance relationship between ten well-known existing energy-based pseudoknot-free RNA secondary structure prediction methods and clearly demonstrate the progress that has been achieved in recent years. Secondly, we introduce AveRNA, a generic and powerful method for combining a set of existing secondary structure prediction procedures into an ensemble-based method that achieves significantly higher prediction accuracies than obtained from any of its component procedures. Our new, ensemble-based method, AveRNA, improves the state of the art for energy-based, pseudoknot-free RNA secondary structure prediction by exploiting the complementary strengths of multiple existing prediction procedures, as demonstrated using a state-of-the-art statistical resampling approach. In addition, AveRNA allows an intuitive and effective control of the trade-off between false negative and false positive base pair predictions. Finally, AveRNA can make use of arbitrary sets of secondary structure prediction procedures and can therefore be used to leverage improvements in prediction accuracy offered by algorithms and energy models developed in the future. Our data, MATLAB software and a web-based version of AveRNA are publicly available at http://www.cs.ubc.ca/labs/beta/Software/AveRNA.

RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation.

PubMed

Li, Ying; Shi, Xiaohu; Liang, Yanchun; Xie, Juan; Zhang, Yu; Ma, Qin

2017-01-21

RNAs have been found to carry diverse functionalities in nature. Inferring the similarity between two given RNAs is a fundamental step to understand and interpret their functional relationship. The majority of functional RNAs show conserved secondary structures, rather than sequence conservation. Those algorithms relying on sequence-based features usually have limitations in their prediction performance. Hence, integrating RNA structure features is very critical for RNA analysis. Existing algorithms mainly fall into two categories: alignment-based and alignment-free. The alignment-free algorithms of RNA comparison usually have lower time complexity than alignment-based algorithms. An alignment-free RNA comparison algorithm was proposed, in which novel numerical representations RNA-TVcurve (triple vector curve representation) of RNA sequence and corresponding secondary structure features are provided. Then a multi-scale similarity score of two given RNAs was designed based on wavelet decomposition of their numerical representation. In support of RNA mutation and phylogenetic analysis, a web server (RNA-TVcurve) was designed based on this alignment-free RNA comparison algorithm. It provides three functional modules: 1) visualization of numerical representation of RNA secondary structure; 2) detection of single-point mutation based on secondary structure; and 3) comparison of pairwise and multiple RNA secondary structures. The inputs of the web server require RNA primary sequences, while corresponding secondary structures are optional. For the primary sequences alone, the web server can compute the secondary structures using free energy minimization algorithm in terms of RNAfold tool from Vienna RNA package. RNA-TVcurve is the first integrated web server, based on an alignment-free method, to deliver a suite of RNA analysis functions, including visualization, mutation analysis and multiple RNAs structure comparison. The comparison results with two popular RNA comparison tools, RNApdist and RNAdistance, showcased that RNA-TVcurve can efficiently capture subtle relationships among RNAs for mutation detection and non-coding RNA classification. All the relevant results were shown in an intuitive graphical manner, and can be freely downloaded from this server. RNA-TVcurve, along with test examples and detailed documents, are available at: http://ml.jlu.edu.cn/tvcurve/ .

Molecular Dynamics Analysis of Lysozyme Protein in Ethanol-Water Mixed Solvent Environment

NASA Astrophysics Data System (ADS)

Ochije, Henry Ikechukwu

Effect of protein-solvent interaction on the protein structure is widely studied using both experimental and computational techniques. Despite such extensive studies molecular level understanding of proteins and some simple solvents is still not fully understood. This work focuses on detailed molecular dynamics simulations to study of solvent effect on lysozyme protein, using water, alcohol and different concentrations of water-alcohol mixtures as solvents. The lysozyme protein structure in water, alcohol and alcohol-water mixture (0-12% alcohol) was studied using GROMACS molecular dynamics simulation code. Compared to water environment, the lysozome structure showed remarkable changes in solvents with increasing alcohol concentration. In particular, significant changes were observed in the protein secondary structure involving alpha helices. The influence of alcohol on the lysozyme protein was investigated by studying thermodynamic and structural properties. With increasing ethanol concentration we observed a systematic increase in total energy, enthalpy, root mean square deviation (RMSD), and radius of gyration. a polynomial interpolation approach. Using the resulting polynomial equation, we could determine above quantities for any intermediate alcohol percentage. In order to validate this approach, we selected an intermediate ethanol percentage and carried out full MD simulation. The results from MD simulation were in reasonably good agreement with that obtained using polynomial approach. Hence, the polynomial approach based method proposed here eliminates the need for computationally intensive full MD analysis for the concentrations within the range (0-12%) studied in this work.

Genomics of Secondary Metabolism in Populus: Interactions with Biotic and Abiotic Environments

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

Chen, F.; Liu, C.; Tschaplinski, T. J.

2009-09-01

Populus trees face constant challenges from the environment during their life cycle. To ensure their survival and reproduction, Populus trees deploy various types of defenses, one of which is the production of a myriad of secondary metabolites. Compounds derived from the shikimate-phenylpropanoid pathway are the most abundant class of secondary metabolites synthesized in Populus. Among other major classes of secondary metabolites in Populus are terpenoids and fatty acid-derivatives. Some of the secondary metabolites made by Populus trees have been functionally characterized. Some others have been associated with certain biological/ecological processes, such as defense against insects and microbial pathogens or acclimationmore » or adaptation to abiotic stresses. Functions of many Populus secondary metabolites remain unclear. The advent of various novel genomic tools will enable us to explore in greater detail the complexity of secondary metabolism in Populus. Detailed data mining of the Populus genome sequence can unveil candidate genes of secondary metabolism. Metabolomic analysis will continue to identify new metabolites synthesized in Populus. Integrated genomics that combines various 'omics' tools will prove to be the most powerful approach in revealing the molecular and biochemical basis underlying the biosynthesis of secondary metabolites in Populus. Characterization of the biological/ecological functions of secondary metabolites as well as their biosynthesis will provide knowledge and tools for genetically engineering the production of seconday metabolites that can lead to the generation of novel, improved Populus varieties.« less

Native aggregation as a cause of origin of temporary cellular structures needed for all forms of cellular activity, signaling and transformations.

PubMed

Matveev, Vladimir V

2010-06-09

According to the hypothesis explored in this paper, native aggregation is genetically controlled (programmed) reversible aggregation that occurs when interacting proteins form new temporary structures through highly specific interactions. It is assumed that Anfinsen's dogma may be extended to protein aggregation: composition and amino acid sequence determine not only the secondary and tertiary structure of single protein, but also the structure of protein aggregates (associates). Cell function is considered as a transition between two states (two states model), the resting state and state of activity (this applies to the cell as a whole and to its individual structures). In the resting state, the key proteins are found in the following inactive forms: natively unfolded and globular. When the cell is activated, secondary structures appear in natively unfolded proteins (including unfolded regions in other proteins), and globular proteins begin to melt and their secondary structures become available for interaction with the secondary structures of other proteins. These temporary secondary structures provide a means for highly specific interactions between proteins. As a result, native aggregation creates temporary structures necessary for cell activity."One of the principal objects of theoretical research in any department of knowledge is to find the point of view from which the subject appears in its greatest simplicity."Josiah Willard Gibbs (1839-1903).

Measuring the environmental effects of organic farming: A meta-analysis of structural variables in empirical research.

PubMed

Lee, Ki Song; Choe, Young Chan; Park, Sung Hee

2015-10-01

This study examined the structural variables affecting the environmental effects of organic farming compared to those of conventional farming. A meta-analysis based on 107 studies and 360 observations published from 1977 to 2012 compared energy efficiency (EE) and greenhouse gas emissions (GHGE) for organic and conventional farming. The meta-analysis systematically analyzed the results of earlier comparative studies and used logistic regression to identify the structural variables that contributed to differences in the effects of organic and conventional farming on the environment. The statistical evidence identified characteristics that differentiated the environmental effects of organic and conventional farming, which is controversial. The results indicated that data sources, sample size and product type significantly affected EE, whereas product type, cropping pattern and measurement unit significantly affected the GHGE of organic farming compared to conventional farming. Superior effects of organic farming on the environment were more likely to appear for larger samples, primary data rather than secondary data, monocropping rather than multicropping, and crops other than fruits and vegetables. The environmental effects of organic farming were not affected by the study period, geographic location, farm size, cropping pattern, or measurement method. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Direct Numerical Simulations of Small-Scale Gravity Wave Instability Dynamics in Variable Stratification and Shear

NASA Astrophysics Data System (ADS)

Mixa, T.; Fritts, D. C.; Laughman, B.; Wang, L.; Kantha, L. H.

2015-12-01

Multiple observations provide compelling evidence that gravity wave dissipation events often occur in multi-scale environments having highly-structured wind and stability profiles extending from the stable boundary layer into the mesosphere and lower thermosphere. Such events tend to be highly localized and thus yield local energy and momentum deposition and efficient secondary gravity wave generation expected to have strong influences at higher altitudes [e.g., Fritts et al., 2013; Baumgarten and Fritts, 2014]. Lidars, radars, and airglow imagers typically cannot achieve the spatial resolution needed to fully quantify these small-scale instability dynamics. Hence, we employ high-resolution modeling to explore these dynamics in representative environments. Specifically, we describe numerical studies of gravity wave packets impinging on a sheet of high stratification and shear and the resulting instabilities and impacts on the gravity wave amplitude and momentum flux for various flow and gravity wave parameters. References: Baumgarten, Gerd, and David C. Fritts (2014). Quantifying Kelvin-Helmholtz instability dynamics observed in noctilucent clouds: 1. Methods and observations. Journal of Geophysical Research: Atmospheres, 119.15, 9324-9337. Fritts, D. C., Wang, L., & Werne, J. A. (2013). Gravity wave-fine structure interactions. Part I: Influences of fine structure form and orientation on flow evolution and instability. Journal of the Atmospheric Sciences, 70(12), 3710-3734.

Optimising the management of severe Traumatic Brain Injury in the military maritime environment.

PubMed

Edgar, I A; Hadjipavlou, G; Smith, J E

2014-01-01

Severe Traumatic Brain Injury (sTBI) is a devastating cause of morbidity and mortality, especially among those aged less than 45 years. Advances in clinical practice continue to focus on preventing primary injury through developing ballistic head and eye protection, and through minimising secondary brain injury (secondary prevention). Managing sTBI is challenging in well-developed, well-resourced healthcare systems. Achieving management aims in the military maritime environment poses even greater challenges. Strategies for the management of sTBI in the maritime environment should be in keeping with current best evidence. Provision of specialist interventions for sTBI in military maritime environments may require alternative approaches matched to the skills of the staff and environmental restrictions.

Changing from primary to secondary school highlights opportunities for school environment interventions aiming to increase physical activity and reduce sedentary behaviour: a longitudinal cohort study.

PubMed

Marks, Jennifer; Barnett, Lisa M; Strugnell, Claudia; Allender, Steven

2015-05-08

There is little empirical evidence of the impact of transition from primary to secondary school on obesity-related risk behaviour. The purpose of this study was to examine the effect of a change of school system on physical activity (PA) and sedentary behaviour in pre-early adolescents. Fifteen schools in Victoria, Australia were recruited at random from the bottom two strata of a five level socio-economic scale. In nine schools, students in year 6 primary school transitioned to a different school for year 7 secondary school, while in six schools (combined primary-secondary), students remained in the same school environment from year 6 to year 7. Time 1 (T1) measures were collected from students (N=245) in year 6 (age 11-13). Time 2 (T2) data were collected from 243 (99%) of the original student cohort when in year 7. PA and sedentary behaviour data were collected objectively (via ActiGraph accelerometer) and subjectively (via child self-report recall questionnaire). School environment data were collected via school staff survey. Change of behaviour analyses were conducted longitudinally i) for all students and ii) by change/no change of school. Mixed model regression analysis tested for behavioural interaction effects of changing/not changing school. Sixty-three percent (N=152) changed schools from T1 to T2. Across all students we observed declines in average daily moderate to vigorous physical activity (MVPA) (-4 min) and light PA (-23 min), and increases in average daily sedentary behaviour (16 min), weekday leisure screen time (17 min) and weekday homework screen time (25 min), all P<0.05. Compared to students who remained in the same school environment, students who changed school reported a greater reduction in PA intensity at recess and lunch, less likelihood to cycle to/from school, greater increase in weekday (41 mins) and weekend (45 mins) leisure screen time (P<0.05) and greater encouragement to participate in sport. School staff surveys identified that sport participation encouragement was greater in primary and combined primary-secondary than secondary schools (P<0.05). Transitioning from primary to secondary school negatively impacts on children's PA and sedentary behaviour, and has further compounding effects on behaviour type by changing school environments.

Effect of Secondary Cooling Conditions on Solidification Structure and Central Macrosegregation in Continuously Cast High-Carbon Rectangular Billet

NASA Astrophysics Data System (ADS)

Zeng, Jie; Chen, Weiqing

2015-10-01

Solidification structures of high carbon rectangular billet with a size of 180 mm × 240 mm in different secondary cooling conditions were simulated using cellular automaton-finite element (CAFE) coupling model. The adequacy of the model was compared with the simulated and the actual macrostructures of 82B steel. Effects of the secondary cooling water intensity on solidification structures including the equiaxed grain ratio and the equiaxed grain compactness were discussed. It was shown that the equiaxed grain ratio and the equiaxed grain compactness changed in the opposite direction at different secondary cooling water intensities. Increasing the secondary cooling water intensity from 0.9 or 1.1 to 1.3 L/kg could improve the equiaxed grain compactness and decrease the equiaxed grain ratio. Besides, the industrial test was conducted to investigate the effect of different secondary cooling water intensities on the center carbon macrosegregation of 82B steel. The optimum secondary cooling water intensity was 0.9 L/kg, while the center carbon segregation degree was 1.10. The relationship between solidification structure and center carbon segregation was discussed based on the simulation results and the industrial test.

40 CFR 50.10 - National 8-hour primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2012 CFR

2012-07-01

... ambient air quality standards for ozone. 50.10 Section 50.10 Protection of Environment ENVIRONMENTAL....10 National 8-hour primary and secondary ambient air quality standards for ozone. (a) The level of the national 8-hour primary and secondary ambient air quality standards for ozone, measured by a...

40 CFR 50.9 - National 1-hour primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2013 CFR

2013-07-01

... ambient air quality standards for ozone. 50.9 Section 50.9 Protection of Environment ENVIRONMENTAL....9 National 1-hour primary and secondary ambient air quality standards for ozone. (a) The level of the national 1-hour primary and secondary ambient air quality standards for ozone measured by a...

40 CFR 50.10 - National 8-hour primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2011 CFR

2011-07-01

... ambient air quality standards for ozone. 50.10 Section 50.10 Protection of Environment ENVIRONMENTAL....10 National 8-hour primary and secondary ambient air quality standards for ozone. (a) The level of the national 8-hour primary and secondary ambient air quality standards for ozone, measured by a...

40 CFR 50.9 - National 1-hour primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2012 CFR

2012-07-01

... ambient air quality standards for ozone. 50.9 Section 50.9 Protection of Environment ENVIRONMENTAL....9 National 1-hour primary and secondary ambient air quality standards for ozone. (a) The level of the national 1-hour primary and secondary ambient air quality standards for ozone measured by a...

40 CFR 50.10 - National 8-hour primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2013 CFR

2013-07-01

... ambient air quality standards for ozone. 50.10 Section 50.10 Protection of Environment ENVIRONMENTAL....10 National 8-hour primary and secondary ambient air quality standards for ozone. (a) The level of the national 8-hour primary and secondary ambient air quality standards for ozone, measured by a...

40 CFR 50.9 - National 1-hour primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2011 CFR

2011-07-01

... ambient air quality standards for ozone. 50.9 Section 50.9 Protection of Environment ENVIRONMENTAL....9 National 1-hour primary and secondary ambient air quality standards for ozone. (a) The level of the national 1-hour primary and secondary ambient air quality standards for ozone measured by a...

40 CFR 50.9 - National 1-hour primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2010 CFR

2010-07-01

... ambient air quality standards for ozone. 50.9 Section 50.9 Protection of Environment ENVIRONMENTAL....9 National 1-hour primary and secondary ambient air quality standards for ozone. (a) The level of the national 1-hour primary and secondary ambient air quality standards for ozone measured by a...

40 CFR 50.10 - National 8-hour primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2014 CFR

2014-07-01

... ambient air quality standards for ozone. 50.10 Section 50.10 Protection of Environment ENVIRONMENTAL....10 National 8-hour primary and secondary ambient air quality standards for ozone. (a) The level of the national 8-hour primary and secondary ambient air quality standards for ozone, measured by a...

40 CFR 50.10 - National 8-hour primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2010 CFR

2010-07-01

... ambient air quality standards for ozone. 50.10 Section 50.10 Protection of Environment ENVIRONMENTAL....10 National 8-hour primary and secondary ambient air quality standards for ozone. (a) The level of the national 8-hour primary and secondary ambient air quality standards for ozone, measured by a...

40 CFR 50.9 - National 1-hour primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2014 CFR

2014-07-01

... ambient air quality standards for ozone. 50.9 Section 50.9 Protection of Environment ENVIRONMENTAL....9 National 1-hour primary and secondary ambient air quality standards for ozone. (a) The level of the national 1-hour primary and secondary ambient air quality standards for ozone measured by a...

Research into Students' Perceptions of Preferred and Actual Learning Environment.

ERIC Educational Resources Information Center

Hattie, John A.; And Others

Measures of both preferred and actual classroom and school environment were administered to 1,675 secondary school students in New South Wales (Australia). Shortened versions of the My Class Inventory, Classroom Environment Scale, and Individualized Classroom Environment Questionnaire, as well as the Quality of School Life questionnaire were…

The predicted secondary structures of class I fructose-bisphosphate aldolases.

PubMed Central

Sawyer, L; Fothergill-Gilmore, L A; Freemont, P S

1988-01-01

The results of several secondary-structure prediction programs were combined to produce an estimate of the regions of alpha-helix, beta-sheet and reverse turns for fructose-bisphosphate aldolases from human and rat muscle and liver, from Trypanosoma brucei and from Drosophila melanogaster. All the aldolase sequences gave essentially the same pattern of secondary-structure predictions despite having sequences up to 50% different. One exception to this pattern was an additional strongly predicted helix in the rat liver and Drosophila enzymes. Regions of relatively high sequence variation generally were predicted as reverse turns, and probably occur as surface loops. Most of the positions corresponding to exon boundaries are located between regions predicted to have secondary-structural elements consistent with a compact structure. The predominantly alternating alpha/beta structure predicted is consistent with the alpha/beta-barrel structure indicated by preliminary high-resolution X-ray diffraction studies on rabbit muscle aldolase [Sygusch, Beaudry & Allaire (1986) Biophys. J. 49, 287a]. Images Fig. 1. (cont.) Fig. 1. PMID:3128269

Testing Mediation Using Multiple Regression and Structural Equation Modeling Analyses in Secondary Data

ERIC Educational Resources Information Center

Li, Spencer D.

2011-01-01

Mediation analysis in child and adolescent development research is possible using large secondary data sets. This article provides an overview of two statistical methods commonly used to test mediated effects in secondary analysis: multiple regression and structural equation modeling (SEM). Two empirical studies are presented to illustrate the…

Is change in environmental supportiveness between primary and secondary school associated with a decline in children׳s physical activity levels?

PubMed

Coombes, Emma; Jones, Andy; Page, Angie; Cooper, Ashley R

2014-09-01

Using a sample of English schoolchildren, we evaluate whether a change in school local area environmental supportiveness between primary and secondary school is associated with changes in active travel behaviours and physical activity levels. Participant׳s activity levels and travel behaviours were recorded for a week during their primary school final year and secondary school first year. Environmental supportiveness was evaluated using a Geographical Information System. Children attending both a primary and secondary school with a more supportive local environment were more likely to maintain active travel behaviours than those with less supportive environments. However, no trends were apparent with change in school supportiveness and change in physical activity. Policies that focus on the maintenance and uptake of active travel behaviours may help maintain children׳s physical activity levels into adolescence. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

A qualitative examination of factors related to the decrease in physical activity behavior in adolescent girls during the transition from primary to secondary school.

PubMed

Knowles, Ann-Marie; Niven, Ailsa; Fawkner, Samantha

2011-11-01

Quantitative research has suggested that the decline in physical activity levels for adolescent girls is most marked during the transition from primary school to secondary school yet understanding the contributing factors for this decline may be advanced through qualitative research methods to gain an individual perspective of the girls' school transition experience. This study explored factors related to the decrease in physical activity behavior in 14 adolescent girls (mean age = 13.6 ± 0.3 years) during the transition between primary and secondary school through the use of narrative interviews and interpretative phenomenological analysis. The findings suggested that a change in the environment was central to understanding the decline in physical activity levels since primary school. During secondary school, a positive environment can be created by ensuring a choice of activities in Physical Education lessons; allowing a girls-only environment, to reduce the focus on competence and competition, and recognizing the importance of social support. These could enhance self-perceptions, reduce self-presentational concerns, increase enjoyment, and subsequently reduce the decrease in physical activity behavior during this key transitional period.

Principles of biofouling protection in marine sponges: a model for the design of novel biomimetic and bio-inspired coatings in the marine environment?

PubMed

Müller, Werner E G; Wang, Xiaohong; Proksch, Peter; Perry, Carole C; Osinga, Ronald; Gardères, Johan; Schröder, Heinz C

2013-08-01

The process of biofouling of marine structures and substrates, such as platforms or ship hulls, proceeds in multiple steps. Soon after the formation of an initial conditioning film, formed via the adsorption of organic particles to natural or man-made substrates, a population of different bacterial taxa associates under the formation of a biofilm. These microorganisms communicate through a complex quorum sensing network. Macro-foulers, e.g., barnacles, then settle and form a fouling layer on the marine surfaces, a process that globally has severe impacts both on the economy and on the environment. Since the ban of tributyltin, an efficient replacement of this antifouling compound by next-generation antifouling coatings that are environmentally more acceptable and also showing longer half-lives has not yet been developed. The sponges, as sessile filter-feeder animals, have evolved antifouling strategies to protect themselves against micro- and subsequent macro-biofouling processes. Experimental data are summarized and suggest that coating of the sponge surface with bio-silica contributes to the inhibition of the formation of a conditioning film. A direct adsorption of the surfaces by microorganisms can be impaired through poisoning the organisms with direct-acting secondary metabolites or toxic peptides. In addition, first, compounds from sponges have been identified that interfere with the anti-quorum sensing network. Sponge secondary metabolites acting selectively on diatom colonization have not yet been identified. Finally, it is outlined that direct-acting secondary metabolites inhibiting the growth of macro-fouling animals and those that poison the multidrug resistance pump are available. It is concluded that rational screening programs for inhibitors of the complex and dynamic problem of biofilm production, based on multidisciplinary studies and using sponges as a model, are required in the future.

The weathering and transformation process of lead in China's shooting ranges.

PubMed

Li, Yeling; Zhu, Yongbing; Zhao, Sanping; Liu, Xiaodong

2015-09-01

Corroding steel-core bullets from three shooting ranges in different climate zones of China were collected. Multiple technical methods (EMPA, SEM, XRD, and ICP-OES) were applied to investigate the structure, morphology, and weathering product of this type of bullet in China to analyze the weathering mechanisms in different types of soils. A scanning electron microscope (SEM) was used to view the morphology and microstructure of corrosion layers. On the corroded lead layer surface, unevenness, micro cracks, and spallation were usually present. Around the micro cracks, many types of euhedral and subhedral crystals of the secondary products of lead were formed, most of which were composed of cerussite (PbCO3), while hydrocerussite (Pb3(CO3)2(OH)2) was predominant in the bullet collected from the humid environment. X-ray power diffraction (XRD) results show that the secondary weathering products in the three shooting range soils are clearly different. In the Fangyan shooting range, which has a neutral and semi-arid soil, the lead weathering product was mainly hydrocerussite (Pb3(CO3)2(OH)2), while no substantial amount of crystal phase of lead compound could be found in acidic, damp soils from the Fenghuang shooting range, possibly due to the enhanced dissolution and mobilization of lead compounds at lower pH and higher content of organic matter in the soil. In hot and arid environment of the Baicheng shooting range, cerussite might have undergone thermal decomposition, thus generating shannonite (Pb2O(CO3)). These results indicate that the formation of secondary Pb minerals is largely affected by the climatic zone or the soil properties, which may have implications for range management practices.

In Situ Infrared Ellipsometry for Protein Adsorption Studies on Ultrathin Smart Polymer Brushes in Aqueous Environment

DOE PAGES

Kroning, Annika; Furchner, Andreas; Aulich, Dennis; ...

2015-02-10

The protein-adsorbing and -repelling properties of various smart nanometer-thin polymer brushes with high potential for biosensing and biomedical applications are studied by in-situ infrared-spectroscopic ellipsometry (IRSE). IRSE as a highly sensitive non-destructive technique allows us to investigate protein adsorption on polymer brushes in aqueous environment in dependence of external stimuli like temperature and pH. These stimuli are, for instance, relevant in switchable mixed brushes containing poly(N-isopropyl acrylamide) and poly(acrylic acid), respectively. We use such brushes as model surfaces for controlling protein adsorption of human serum albumin and human fibrinogen. IRSE can distinguish between polymer-specific vibrational bands, which yield insights intomore » the hydration state of the brushes, and changes in the protein-specific amide bands, which are related to changes of the protein secondary structure.« less

[Soil mesofauna in differents systems of land use soil in Upper River Solimões, AM, Brazil].

PubMed

Morais, José W De; Oliveira, Viviane Dos S; Dambros, Cristian De S; Tapia-Coral, Sandra C; Acioli, Agno N S

2010-01-01

The mesofauna has an important function in the soil and it is represented mainly by Acari Oribatida and Collembola. We report the first data on the density and diversity of the soil mesofauna in Benjamin Constant, Amazonas State, Brazil. The following systems were evaluated: primary forest, secondary forest, agroforestry system, cultivated areas and pastures. A total of 101 samples were collected 100 m apart from each other and specimens were collected by using Berlese-Tullgren method. The highest density was registered in secondary forest (29,776 specimens.m-2). Acari Oribatida was the dominant group (7.072 specimens.m-2) in the pasture, suggesting that mites show higher capacity of adaptation to disturbed environments and/or due to the presence of gregarious species. The density of Collembola (5,632 specimens.m-2) was higher in secondary forest. Formicidae was the dominant group (27,824 specimens.m-2) and its highest density occurred in the secondary forest (12,336 specimens.m-2). Seven species and ten morphospecies of Isoptera and three species of Symphyla were identified. The highest density and diversity were found in secondary forest. One supposes that the low density of mesofauna found in all of the studied systems is being influenced by soil structure and composition as well as litter volume. For SUT, the composition of taxonomic groups in the cultivated areas is similar to the one found in primary forest, while the groups found in the agroforestry system are similar to those in the pasture, which may help to decide on land use strategies.

A secondary copulatory structure in a female insect: a clasp for a nuptial meal?

NASA Astrophysics Data System (ADS)

Gwynne, Darryl T.

2002-03-01

Secondary copulatory structures are well-known in male dragonflies and spiders. Here I report a secondary copulatory organ in female ground weta, Hemiandrus pallitarsis (Ensifera, Orthoptera - crickets and allies). The organ, located on the underside of the abdomen, appears to secure the male's genitalia during the transfer of a spermatophylax nuptial meal to this location, an area quite separate from the female's primary copulatory structures, where the sperm ampulla is attached.

RNA Secondary Structure Prediction by Using Discrete Mathematics: An Interdisciplinary Research Experience for Undergraduate Students

PubMed Central

Ellington, Roni; Wachira, James

2010-01-01

The focus of this Research Experience for Undergraduates (REU) project was on RNA secondary structure prediction by using a lattice walk approach. The lattice walk approach is a combinatorial and computational biology method used to enumerate possible secondary structures and predict RNA secondary structure from RNA sequences. The method uses discrete mathematical techniques and identifies specified base pairs as parameters. The goal of the REU was to introduce upper-level undergraduate students to the principles and challenges of interdisciplinary research in molecular biology and discrete mathematics. At the beginning of the project, students from the biology and mathematics departments of a mid-sized university received instruction on the role of secondary structure in the function of eukaryotic RNAs and RNA viruses, RNA related to combinatorics, and the National Center for Biotechnology Information resources. The student research projects focused on RNA secondary structure prediction on a regulatory region of the yellow fever virus RNA genome and on an untranslated region of an mRNA of a gene associated with the neurological disorder epilepsy. At the end of the project, the REU students gave poster and oral presentations, and they submitted written final project reports to the program director. The outcome of the REU was that the students gained transferable knowledge and skills in bioinformatics and an awareness of the applications of discrete mathematics to biological research problems. PMID:20810968

RNA secondary structure prediction by using discrete mathematics: an interdisciplinary research experience for undergraduate students.

PubMed

Ellington, Roni; Wachira, James; Nkwanta, Asamoah

2010-01-01

The focus of this Research Experience for Undergraduates (REU) project was on RNA secondary structure prediction by using a lattice walk approach. The lattice walk approach is a combinatorial and computational biology method used to enumerate possible secondary structures and predict RNA secondary structure from RNA sequences. The method uses discrete mathematical techniques and identifies specified base pairs as parameters. The goal of the REU was to introduce upper-level undergraduate students to the principles and challenges of interdisciplinary research in molecular biology and discrete mathematics. At the beginning of the project, students from the biology and mathematics departments of a mid-sized university received instruction on the role of secondary structure in the function of eukaryotic RNAs and RNA viruses, RNA related to combinatorics, and the National Center for Biotechnology Information resources. The student research projects focused on RNA secondary structure prediction on a regulatory region of the yellow fever virus RNA genome and on an untranslated region of an mRNA of a gene associated with the neurological disorder epilepsy. At the end of the project, the REU students gave poster and oral presentations, and they submitted written final project reports to the program director. The outcome of the REU was that the students gained transferable knowledge and skills in bioinformatics and an awareness of the applications of discrete mathematics to biological research problems.

Structure of poly(ethylene glycol)-modified horseradish peroxidase in organic solvents: infrared amide I spectral changes upon protein dehydration are largely caused by protein structural changes and not by water removal per se.

PubMed Central

Al-Azzam, Wasfi; Pastrana, Emil A; Ferrer, Yancy; Huang, Qing; Schweitzer-Stenner, Reinhard; Griebenow, Kai

2002-01-01

Fourier transform infrared (FTIR) spectroscopy has emerged as a powerful tool to guide the development of stable lyophilized protein formulations by providing information on the structure of proteins in amorphous solids. The underlying assumption is that IR spectral changes in the amide I and III region upon protein dehydration are caused by protein structural changes. However, it has been claimed that amide I IR spectral changes could be the result of water removal per se. Here, we investigated whether such claims hold true. The structure of horseradish peroxidase (HRP) and poly(ethylene glycol)-modified HRP (HRP-PEG) has been investigated under various conditions (in aqueous solution, the amorphous dehydrated state, and dissolved/suspended in toluene and benzene) by UV-visible (UV-Vis), FTIR, and resonance Raman spectroscopy. The resonance Raman and UV-Vis spectra of dehydrated HRP-PEG dissolved in neat toluene or benzene were very similar to that of HRP in aqueous buffer, and thus the heme environment (heme iron spin, coordination, and redox state) was essentially the same under both conditions. Therefore, the three-dimensional structure of HRP-PEG dissolved in benzene and toluene was similar to that in aqueous solution. The amide I IR spectra of HRP-PEG in aqueous buffer and of dehydrated HRP-PEG dissolved in neat benzene and toluene were also very similar, and the secondary structure compositions (percentages of alpha-helices and beta-sheets) were within the standard error the same. These results are irreconcilable with recent claims that water removal per se could cause substantial amide I IR spectral changes (M. van de Weert, P.I. Haris, W.E. Hennink, and D.J. Crommelin. 2001. Anal. Biochem. 297:160-169). On the contrary, amide I IR spectral changes upon protein dehydration are caused by perturbations in the secondary structure. PMID:12496131

Stability of Secondary and Tertiary Structures of Virus-Like Particles Representing Noroviruses: Effects of pH, Ionic Strength, and Temperature and Implications for Adhesion to Surfaces.

PubMed

Samandoulgou, Idrissa; Hammami, Riadh; Morales Rayas, Rocio; Fliss, Ismail; Jean, Julie

2015-11-01

Loss of ordered molecular structure in proteins is known to increase their adhesion to surfaces. The aim of this work was to study the stability of norovirus secondary and tertiary structures and its implications for viral adhesion to fresh foods and agrifood surfaces. The pH, ionic strength, and temperature conditions studied correspond to those prevalent in the principal vehicles of viral transmission (vomit and feces) and in the food processing and handling environment (pasteurization and refrigeration). The structures of virus-like particles representing GI.1, GII.4, and feline calicivirus (FCV) were studied using circular dichroism and intrinsic UV fluorescence. The particles were remarkably stable under most of the conditions. However, heating to 65°C caused losses of β-strand structure, notably in GI.1 and FCV, while at 75°C the α-helix content of GII.4 and FCV decreased and tertiary structures unfolded in all three cases. Combining temperature with pH or ionic strength caused variable losses of structure depending on the particle type. Regardless of pH, heating to pasteurization temperatures or higher would be required to increase GII.4 and FCV adhesion, while either low or high temperatures would favor GI.1 adhesion. Regardless of temperature, increased ionic strength would increase GII.4 adhesion but would decrease GI.1 adhesion. FCV adsorption would be greater at refrigeration, pasteurization, or high temperature combined with a low salt concentration or at a higher NaCl concentration regardless of temperature. Norovirus adhesion mediated by hydrophobic interaction may depend on hydrophobic residues normally exposed on the capsid surface at pH 3, pH 8, physiological ionic strength, and low temperature, while at pasteurization temperatures it may rely more on buried hydrophobic residues exposed upon structural rearrangement. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Secondary ion mass spectrometric investigation on ruthenium oxide systems: a comparison between poly- and nanocrystalline deposits

PubMed

Barison; Barreca; Daolio; Fabrizio; Piccirillo

2000-01-01

The influence of different RuO(2) crystallite sizes was investigated by secondary ion mass spectrometry (SIMS) on the oxide deposited on various support materials (Ni, Ti, Al(2)O(3), oxidized Si(100)). In order to examine the effect of an oxidic environment on the film structure, RuO(2) 20%-TiO(2) 80% at. mixed oxide was deposited on Ti. The polycrystalline coatings were prepared by heating the Ru (and Ti)-containing solution dropped on the supports.1 RuO(2) nanocrystalline coatings were grown by chemical vapor deposition (CVD) from Ru(COD)(eta(3)-allyl)(2).2 The identification of mixed oxide clusters showed the higher reactivity of Ni and Al(2)O(3) over the other substrates. Diffusion and migration characteristics were observed to be influenced by the nature of the support. The results are complementary to those of a previous SIMS investigation.3 Copyright 2000 John Wiley & Sons, Ltd.

Influence of secondary structure on in-source decay of protein in matrix-assisted laser desorption/ionization mass spectrometry.

PubMed

Takayama, Mitsuo; Osaka, Issey; Sakakura, Motoshi

2012-01-01

The susceptibility of the N-Cα bond of the peptide backbone to specific cleavage by in-source decay (ISD) in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) was studied from the standpoint of the secondary structure of three proteins. A naphthalene derivative, 5-amino-1-naphtol (5,1-ANL), was used as the matrix. The resulting c'-ions, which originate from the cleavage at N-Cα bonds in flexible secondary structures such as turn and bend, and are free from intra-molecular hydrogen-bonded α-helix structure, gave relatively intense peaks. Furthermore, ISD spectra of the proteins showed that the N-Cα bonds of specific amino acid residues, namely Gly-Xxx, Xxx-Asp, and Xxx-Asn, were more susceptible to MALDI-ISD than other amino acid residues. This is in agreement with the observation that Gly, Asp and Asn residues usually located in turns, rather than α-helix. The results obtained indicate that protein molecules embedded into the matrix crystal in the MALDI experiments maintain their secondary structures as determined by X-ray crystallography, and that MALDI-ISD has the capability for providing information concerning the secondary structure of protein.

Passive Isolators for use on the International Space Station

NASA Technical Reports Server (NTRS)

Houston, Janice; Gattis, Christy

2003-01-01

The value of the International Space Station (ISS) as a premier microgravity environment is currently at risk due to structure-borne vibration. The vibration sources are varied and include crew activities such as exercising or simply moving from module to module, and electro- mechanical equipment such as fans and pumps. Given such potential degradation of usable microgravity, anything that can be done to dampen vibration on-orbit will significantly benefit microgravity users. Most vibration isolation schemes, both active and passive, have proven to be expensive - both operationally and from the cost of integrating isolation systems into primary/secondary structural interfaces (e.g., the ISS module/rack interface). Recently, passively absorptive materials have been tested at the bolt interfaces between the operating equipment and support structure (secondary/tertiary structural interfaces). The results indicate that these materials may prove cost-effective in mitigating the vibrational problems of the ISS. We report herein tests of passive absorbers placed at the interface of a vibration-inducing component: the Development Distillation Assembly, a subassembly of the Urine Processing Assembly, which is a rotating centrifuge and cylinder assembly attached to a mounting plate. Passive isolators were installed between this mounting plate and its support shelf. Three materials were tested: BISCO HT-800, Sorbothane 30 and Sorbothane 50, plus a control test with a hard shim. In addition, four distinct combinations of the HT-800 and Sorbothane 50 were tested. Results show a significant (three orders of magnitude) reduction of transmitted energy, as measured in power spectral density (PSD), using the isolation materials. It is noted, however, that passive materials cannot prevent the transmission of very strong forces or absorb the total energy induced from structural resonances.

Amyloid-β peptide structure in aqueous solution varies with fragment size

NASA Astrophysics Data System (ADS)

Wise-Scira, Olivia; Xu, Liang; Kitahara, Taizo; Perry, George; Coskuner, Orkid

2011-11-01

Various fragment sizes of the amyloid-β (Aβ) peptide have been utilized to mimic the properties of the full-length Aβ peptide in solution. Among these smaller fragments, Aβ16 and Aβ28 have been investigated extensively. In this work, we report the structural and thermodynamic properties of the Aβ16, Aβ28, and Aβ42 peptides in an aqueous solution environment. We performed replica exchange molecular dynamics simulations along with thermodynamic calculations for investigating the conformational free energies, secondary and tertiary structures of the Aβ16, Aβ28, and Aβ42 peptides. The results show that the thermodynamic properties vary from each other for these peptides. Furthermore, the secondary structures in the Asp1-Lys16 and Asp1-Lys28 regions of Aβ42 cannot be completely captured by the Aβ16 and Aβ28 fragments. For example, the β-sheet structures in the N-terminal region of Aβ16 and Aβ28 are either not present or the abundance is significantly decreased in Aβ42. The α-helix and β-sheet abundances in Aβ28 and Aβ42 show trends - to some extent - with the potential of mean forces but no such trend could be obtained for Aβ16. Interestingly, Arg5 forms salt bridges with large abundances in all three peptides. The formation of a salt bridge between Asp23-Lys28 is more preferred over the Glu22-Lys28 salt bridge in Aβ28 but this trend is vice versa for Aβ42. This study shows that the Asp1-Lys16 and Asp1-Lys28 regions of the full length Aβ42 peptide cannot be completely mimicked by studying the Aβ16 and Aβ28 peptides.

Collagencin, an antibacterial peptide from fish collagen: Activity, structure and interaction dynamics with membrane

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

Ennaas, Nadia; Hammami, Riadh, E-mail: riadh.hammami@fsaa.ulaval.ca; Gomaa, Ahmed

In this study, we first report characterization of collagencin, an antimicrobial peptide identified from fish collagen hydrolysate. The peptide completely inhibited the growth of Staphylococcus aureus at 1.88 mM. Although non-toxic up to 470 μM, collagencin was hemolytic at higher concentrations. The secondary structure of collagencin was mainly composed by β-sheet and β-turn as determined by CD measurements and molecular dynamics. The peptide is likely to form β-sheet structure under hydrophobic environments and interacts with both anionic (phosphatidylglycerol) and zwitterionic (phosphoethanolamine and phosphatidylcholine) lipids as shown with CD spectroscopy and molecular dynamics. The peptide formed several hydrogen bonds with both POPG andmore » POPE lipids and remained at membrane–water interface, suggesting that collagencin antibacterial action follows a carpet mechanism. Collagenous fish wastes could be processed by enzymatic hydrolysis and transformed into products of high value having functional or biological properties. Marine collagens are a promising source of antimicrobial peptides with new implications in food safety and human health. - Highlights: • Collagencin, an antibacterial (G+ & G-) peptide identified from fish collagen hydrolysate. • The peptide completely inhibited the growth of S. aureus at 1.88 mM and non-toxic at 470 μM. • The secondary structure was mainly composed by β-sheet and turn as determined by CD and MD. • Collagencin interacts with both anionic and zwitterionic lipids as shown with CD and MD. • Collagencin antibacterial action probably follows a carpet mechanism.« less

Revisiting and re-engineering the classical zinc finger peptide: consensus peptide-1 (CP-1).

PubMed

Besold, Angelique N; Widger, Leland R; Namuswe, Frances; Michalek, Jamie L; Michel, Sarah L J; Goldberg, David P

2016-04-01

Zinc plays key structural and catalytic roles in biology. Structural zinc sites are often referred to as zinc finger (ZF) sites, and the classical ZF contains a Cys2His2 motif that is involved in coordinating Zn(II). An optimized Cys2His2 ZF, named consensus peptide 1 (CP-1), was identified more than 20 years ago using a limited set of sequenced proteins. We have reexamined the CP-1 sequence, using our current, much larger database of sequenced proteins that have been identified from high-throughput sequencing methods, and found the sequence to be largely unchanged. The CCHH ligand set of CP-1 was then altered to a CAHH motif to impart hydrolytic activity. This ligand set mimics the His2Cys ligand set of peptide deformylase (PDF), a hydrolytically active M(II)-centered (M = Zn or Fe) protein. The resultant peptide [CP-1(CAHH)] was evaluated for its ability to coordinate Zn(II) and Co(II) ions, adopt secondary structure, and promote hydrolysis. CP-1(CAHH) was found to coordinate Co(II) and Zn(II) and a pentacoordinate geometry for Co(II)-CP-1(CAHH) was implicated from UV-vis data. This suggests a His2Cys(H2O)2 environment at the metal center. The Zn(II)-bound CP-1(CAHH) was shown to adopt partial secondary structure by 1-D (1)H NMR spectroscopy. Both Zn(II)-CP-1(CAHH) and Co(II)-CP-1(CAHH) show good hydrolytic activity toward the test substrate 4-nitrophenyl acetate, exhibiting faster rates than most active synthetic Zn(II) complexes.

Selection of Drought Tolerant Maize Hybrids Using Path Coefficient Analysis and Selection Index.

PubMed

Dao, Abdalla; Sanou, Jacob; V S Traore, Edgar; Gracen, Vernon; Danquah, Eric Y

2017-01-01

In drought-prone environments, direct selection for yield is not adequate because of the variable environment and genotype x environment interaction. Therefore, the use of secondary traits in addition to yield has been suggested. The relative usefulness of secondary traits as indirect selection criteria for maize grain yield is determined by the magnitudes of their genetic variance, heritability and genetic correlation with the grain yield. Forty eight testcross hybrids derived from lines with different genetic background and geographical origins plus 7 checks were evaluated in both well-watered and water-stressed conditions over two years for grain yield and secondary traits to determine the most appropriate secondary traits and select drought tolerant hybrids. Study found that broad-sense heritability of grain yield and Ear Per Plant (EPP) increased under drought stress. Ear aspect (EASP) and ear height (EHT) had larger correlation coefficients and direct effect on grain yield but in opposite direction, negative and positive respectively. Traits like, EPP, Tassel Size (TS) and Plant Recovery (PR) contributed to increase yield via EASP by a large negative indirect effect. Under drought stress, EHT had positive and high direct effect and negative indirect effect via plant height on grain yield indicating that the ratio between ear and plant heights (R-EPH) was associated to grain yield. Path coefficient analysis showed that traits EPP, TS, PR, EASP, R-EPH were important secondary traits in the present experiment. These traits were used in a selection index to classify hybrids according to their performance under drought. The selection procedure included also a Relative Decrease in Yield (RDY) index. Some secondary traits reported as significant selection criteria for selection under drought stress were not finally established in the present study. This is because the relationship between grain and secondary traits can be affected by various factors including germplasm, environment and applied statistical analysis. Therefore, different traits and selection procedure should be applied in the selection process of drought tolerant genotypes for diverse genetic materials and growing conditions.

Secondary structure prediction and structure-specific sequence analysis of single-stranded DNA.

PubMed

Dong, F; Allawi, H T; Anderson, T; Neri, B P; Lyamichev, V I

2001-08-01

DNA sequence analysis by oligonucleotide binding is often affected by interference with the secondary structure of the target DNA. Here we describe an approach that improves DNA secondary structure prediction by combining enzymatic probing of DNA by structure-specific 5'-nucleases with an energy minimization algorithm that utilizes the 5'-nuclease cleavage sites as constraints. The method can identify structural differences between two DNA molecules caused by minor sequence variations such as a single nucleotide mutation. It also demonstrates the existence of long-range interactions between DNA regions separated by >300 nt and the formation of multiple alternative structures by a 244 nt DNA molecule. The differences in the secondary structure of DNA molecules revealed by 5'-nuclease probing were used to design structure-specific probes for mutation discrimination that target the regions of structural, rather than sequence, differences. We also demonstrate the performance of structure-specific 'bridge' probes complementary to non-contiguous regions of the target molecule. The structure-specific probes do not require the high stringency binding conditions necessary for methods based on mismatch formation and permit mutation detection at temperatures from 4 to 37 degrees C. Structure-specific sequence analysis is applied for mutation detection in the Mycobacterium tuberculosis katG gene and for genotyping of the hepatitis C virus.

Secondary flow structures in the presence of Type-IV stent fractures through a bent tube model for curved arteries: Effect of circulation thresholding

NASA Astrophysics Data System (ADS)

Hussain, Shadman; Bulusu, Kartik V.; Plesniak, Michael W.

2013-11-01

A common treatment for atherosclerosis is the opening of narrowed arteries resulting from obstructive lesions by angioplasty and stent implantation to restore unrestricted blood flow. ``Type-IV'' stent fractures involve complete transverse, linear fracture of stent struts, along with displacement of the stent fragments. Experimental data pertaining to secondary flows in the presence of stents that underwent ``Type-IV'' fractures in a bent artery model under physiological inflow conditions were obtained through a two-component, two-dimensional (2C-2D) PIV technique. Concomitant stent-induced flow perturbations result in secondary flow structures with complex, multi-scale morphologies and varying size-strength characteristics. Ultimately, these flow structures may have a role to play in restenosis and progression of atherosclerotic plaque. Vortex circulation thresholds were established with the goal of resolving and tracking iso-circulation secondary flow vortical structures and their morphological changes. This allowed for a parametric evaluation and quantitative representation of secondary flow structures undergoing deformation and spatial reorganization. Supported by NSF Grant No. CBET- 0828903 and GW Center for Biomimetics and Bioinspired Engineering.

Control of evaporation by geometry in capillary structures. From confined pillar arrays in a gap radial gradient to phyllotaxy-inspired geometry.

PubMed

Chen, Chen; Duru, Paul; Joseph, Pierre; Geoffroy, Sandrine; Prat, Marc

2017-11-08

Evaporation is a key phenomenon in the natural environment and in many technological systems involving capillary structures. Understanding the evaporation front dynamics enables the evaporation rate from microfluidic devices and porous media to be finely controlled. Of particular interest is the ability to control the position of the front through suitable design of the capillary structure. Here, we show how to design model capillary structures in microfluidic devices so as to control the drying kinetics. This is achieved by acting on the spatial organization of the constrictions that influence the invasion of the structure by the gas phase. Two types of control are demonstrated. The first is intended to control the sequence of primary invasions through the pore space, while the second aims to control the secondary liquid structures: films, bridges, etc., that can form in the region of pore space invaded by the gas phase. It is shown how the latter can be obtained from phyllotaxy-inspired geometry. Our study thus opens up a route toward the control of the evaporation kinetics by means of tailored capillary structures.

Novel recombinant insulin analogue with flexible C-terminus in B chain. NMR structure of biosynthetic engineered A22G-B31K-B32R human insulin monomer in water/acetonitrile solution.

PubMed

Borowicz, Piotr; Bocian, Wojciech; Sitkowski, Jerzy; Bednarek, Elżbieta; Mikiewicz-Syguła, Diana; Błażej-Sosnowska, Sylwia; Bogiel, Monika; Rusek, Dorota; Kurzynoga, Dariusz; Kozerski, Lech

2011-11-01

A tertiary structure of recombinant A22(G)-B31(K)-B32(R)-human insulin monomer (insulin GKR) has been characterized by (1)H, (13)C NMR at natural isotopic abundance using NOESY, TOCSY, (1)H/(13)C-GHSQC, and (1)H/(13)C-GHSQC-TOCSY spectra. Translational diffusion studies indicate the monomer structure in water/acetonitrile (65/35vol.%). CSI analysis confirms existence of secondary structure motifs present in human insulin standard (HIS). Both techniques allow to establish that in this solvent recombinant insulin GKR exists as a monomer. Starting from structures calculated by the program CYANA, two different refinement protocols used molecular dynamics simulated annealing with the program AMBER; in vacuum (AMBER_VC), and including a generalized Born solvent model (AMBER_GB). From these calculations an ensemble of 20 structures of lowest energy was chosen which represents the tertiary structure of studied insulin. Here we present novel insulin with added A22(G) amino acid which interacts with β-turn environment resulting in high flexibility of B chain C-terminus. Copyright © 2011 Elsevier B.V. All rights reserved.

The Relationship between School Connectedness and Mental Health during the Transition to Secondary School: A Path Analysis

ERIC Educational Resources Information Center

Lester, Leanne; Waters, Stacey; Cross, Donna

2013-01-01

During the transition from primary to secondary school, students typically experience a new social environment, moving from primary school with small intact classes throughout the day with one main teacher, to a larger secondary school with teachers, classrooms and often classmates changing throughout the day. During this time, students report a…

Predicted secondary structure similarity in the absence of primary amino acid sequence homology: hepatitis B virus open reading frames.

PubMed Central

Schaeffer, E; Sninsky, J J

1984-01-01

Proteins that are related evolutionarily may have diverged at the level of primary amino acid sequence while maintaining similar secondary structures. Computer analysis has been used to compare the open reading frames of the hepatitis B virus to those of the woodchuck hepatitis virus at the level of amino acid sequence, and to predict the relative hydrophilic character and the secondary structure of putative polypeptides. Similarity is seen at the levels of relative hydrophilicity and secondary structure, in the absence of sequence homology. These data reinforce the proposal that these open reading frames encode viral proteins. Computer analysis of this type can be more generally used to establish structural similarities between proteins that do not share obvious sequence homology as well as to assess whether an open reading frame is fortuitous or codes for a protein. PMID:6585835

Mobile-based biology edutainment application for secondary schools

NASA Astrophysics Data System (ADS)

AL-Modwahi, Ashraf Abbas M.; Kaisara, Onalenna; Parkizkar, Behrang; Habibi Lashkari, Arash

2013-03-01

The high increase of mobile technology is leading to mobilized learning environment, thus making traditional learning to diminish slowly and become inactive and unproductive. Learners worldwide are being attracted to mobile environment more so that it promotes anytime, anywhere learning. Biology as a secondary school subject will be applicable for mobile learning for such a time and generation as this. This paper is therefore an attempt to mobile based biology edutainment system for the students who normally range from the ages of thirteen to sixteen.

Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy

PubMed Central

Micsonai, András; Wien, Frank; Kernya, Linda; Lee, Young-Ho; Goto, Yuji; Réfrégiers, Matthieu; Kardos, József

2015-01-01

Circular dichroism (CD) spectroscopy is a widely used technique for the study of protein structure. Numerous algorithms have been developed for the estimation of the secondary structure composition from the CD spectra. These methods often fail to provide acceptable results on α/β-mixed or β-structure–rich proteins. The problem arises from the spectral diversity of β-structures, which has hitherto been considered as an intrinsic limitation of the technique. The predictions are less reliable for proteins of unusual β-structures such as membrane proteins, protein aggregates, and amyloid fibrils. Here, we show that the parallel/antiparallel orientation and the twisting of the β-sheets account for the observed spectral diversity. We have developed a method called β-structure selection (BeStSel) for the secondary structure estimation that takes into account the twist of β-structures. This method can reliably distinguish parallel and antiparallel β-sheets and accurately estimates the secondary structure for a broad range of proteins. Moreover, the secondary structure components applied by the method are characteristic to the protein fold, and thus the fold can be predicted to the level of topology in the CATH classification from a single CD spectrum. By constructing a web server, we offer a general tool for a quick and reliable structure analysis using conventional CD or synchrotron radiation CD (SRCD) spectroscopy for the protein science research community. The method is especially useful when X-ray or NMR techniques fail. Using BeStSel on data collected by SRCD spectroscopy, we investigated the structure of amyloid fibrils of various disease-related proteins and peptides. PMID:26038575

Secondary ionisations in a wall-less ion-counting nanodosimeter: quantitative analysis and the effect on the comparison of measured and simulated track structure parameters in nanometric volumes

NASA Astrophysics Data System (ADS)

Hilgers, Gerhard; Bug, Marion U.; Gargioni, Elisabetta; Rabus, Hans

2015-10-01

The object of investigation in nanodosimetry is the physical characteristics of the microscopic structure of ionising particle tracks, i.e. the sequence of the interaction types and interaction sites of a primary particle and all its secondaries, which reflects the stochastic nature of the radiation interaction. In view of the upcoming radiation therapy with protons and carbon ions, the ionisation structure of the ion track is of particular interest. Owing to limitations in current detector technology, the only way to determine the ionisation cluster size distribution in a DNA segment is to simulate the particle track structure in condensed matter. This is done using dedicated computer programs based on Monte Carlo procedures simulating the interaction of the primary ions with the target. Hence, there is a need to benchmark these computer codes using suitable experimental data. Ionisation cluster size distributions produced in the nanodosimeter's sensitive volume by monoenergetic protons and alpha particles (with energies between 0.1 MeV and 20 MeV) were measured at the PTB ion accelerator facilities. C3H8 and N2 were alternately used as the working gas. The measured data were compared with the simulation results obtained with the PTB Monte-Carlo code PTra [B. Grosswendt, Radiat. Environ. Biophys. 41, 103 (2002); M.U. Bug, E. Gargioni, H. Nettelbeck, W.Y. Baek, G. Hilgers, A.B. Rosenfeld, H. Rabus, Phys. Rev. E 88, 043308 (2013)]. Measured and simulated characteristics of the particle track structure are generally in good agreement for protons over the entire energy range investigated. For alpha particles with energies higher than the Bragg peak energy, a good agreement can also be seen, whereas for energies lower than the Bragg peak energy differences of as much as 25% occur. Significant deviations are only observed for large ionisation cluster sizes. These deviations can be explained by a background consisting of secondary ions. These ions are produced in the region downstream of the extraction aperture by electrons with a kinetic energy of about 2.5 keV, which are themselves released by ions of the "primary" ionisation cluster hitting an electrode in the ion transport system. Including this background of secondary ions in the simulated cluster size distributions leads to a significantly better agreement between measured and simulated data, especially for large ionisation clusters.

Protein Secondary Structures (alpha-helix and beta-sheet) at a Cellular Levle and Protein Fractions in Relation to Rumen Degradation Behaviours of Protein: A New Approach

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

Yu,P.

2007-01-01

Studying the secondary structure of proteins leads to an understanding of the components that make up a whole protein, and such an understanding of the structure of the whole protein is often vital to understanding its digestive behaviour and nutritive value in animals. The main protein secondary structures are the {alpha}-helix and {beta}-sheet. The percentage of these two structures in protein secondary structures influences protein nutritive value, quality and digestive behaviour. A high percentage of {beta}-sheet structure may partly cause a low access to gastrointestinal digestive enzymes, which results in a low protein value. The objectives of the present studymore » were to use advanced synchrotron-based Fourier transform IR (S-FTIR) microspectroscopy as a new approach to reveal the molecular chemistry of the protein secondary structures of feed tissues affected by heat-processing within intact tissue at a cellular level, and to quantify protein secondary structures using multicomponent peak modelling Gaussian and Lorentzian methods, in relation to protein digestive behaviours and nutritive value in the rumen, which was determined using the Cornell Net Carbohydrate Protein System. The synchrotron-based molecular chemistry research experiment was performed at the National Synchrotron Light Source at Brookhaven National Laboratory, US Department of Energy. The results showed that, with S-FTIR microspectroscopy, the molecular chemistry, ultrastructural chemical make-up and nutritive characteristics could be revealed at a high ultraspatial resolution ({approx}10 {mu}m). S-FTIR microspectroscopy revealed that the secondary structure of protein differed between raw and roasted golden flaxseeds in terms of the percentages and ratio of {alpha}-helixes and {beta}-sheets in the mid-IR range at the cellular level. By using multicomponent peak modelling, the results show that the roasting reduced (P <0.05) the percentage of {alpha}-helixes (from 47.1% to 36.1%: S-FTIR absorption intensity), increased the percentage of {beta}-sheets (from 37.2% to 49.8%: S-FTIR absorption intensity) and reduced the {alpha}-helix to {beta}-sheet ratio (from 0.3 to 0.7) in the golden flaxseeds, which indicated a negative effect of the roasting on protein values, utilisation and bioavailability. These results were proved by the Cornell Net Carbohydrate Protein System in situ animal trial, which also revealed that roasting increased the amount of protein bound to lignin, and well as of the Maillard reaction protein (both of which are poorly used by ruminants), and increased the level of indigestible and undegradable protein in ruminants. The present results demonstrate the potential of highly spatially resolved synchrotron-based infrared microspectroscopy to locate 'pure' protein in feed tissues, and reveal protein secondary structures and digestive behaviour, making a significant step forward in and an important contribution to protein nutritional research. Further study is needed to determine the sensitivities of protein secondary structures to various heat-processing conditions, and to quantify the relationship between protein secondary structures and the nutrient availability and digestive behaviour of various protein sources. Information from the present study arising from the synchrotron-based IR probing of the protein secondary structures of protein sources at the cellular level will be valuable as a guide to maintaining protein quality and predicting digestive behaviours.« less

Academic Performance of Students without Disabilities in the Inclusive Environment

ERIC Educational Resources Information Center

Fruth, Jason D.; Woods, Melanie N.

2015-01-01

This study examines the impact of inclusion on secondary students by focusing on the performance of students without disabilities in the inclusive environment compared to their performance in a segregated environment. Many studies exist demonstrating the positive impact of the inclusive environment on the performance of students with disabilities.…

Using the FLUKA Monte Carlo Code to Simulate the Interactions of Ionizing Radiation with Matter to Assist and Aid Our Understanding of Ground Based Accelerator Testing, Space Hardware Design, and Secondary Space Radiation Environments

NASA Technical Reports Server (NTRS)

Reddell, Brandon

2015-01-01

Designing hardware to operate in the space radiation environment is a very difficult and costly activity. Ground based particle accelerators can be used to test for exposure to the radiation environment, one species at a time, however, the actual space environment cannot be duplicated because of the range of energies and isotropic nature of space radiation. The FLUKA Monte Carlo code is an integrated physics package based at CERN that has been under development for the last 40+ years and includes the most up-to-date fundamental physics theory and particle physics data. This work presents an overview of FLUKA and how it has been used in conjunction with ground based radiation testing for NASA and improve our understanding of secondary particle environments resulting from the interaction of space radiation with matter.

Three-dimensional simulations of cumulus congestus clouds on GATE day 261

NASA Technical Reports Server (NTRS)

Simpson, J.; Van Helvoirt, G.; Mccumber, M.

1982-01-01

Schlesinger's (1978) three-dimensional cumulus model is applied to showering congestus clouds on day 261 of GATE. Model results are compared with each other and with observations to analyze the effects of varying shear and altered sounding. Relationships between shear, mesovortices and dynamic entrainment are examined, as well as the model clouds' impact on the environment as a function of shear. The simulations appear to resemble reality in many important aspects. Altostratus layers observed on day 261 are found to be a by-product of convection in three-dimensional shear. Rapid erosion of cloud base to 3.6 km is related to the ambient thermal structure, with wind shear and initial perturbation playing a secondary role. Some of the apparent conflict regarding lateral versus cloud-top entrainment is clarified, as well as some factors governing convective downdraft structure and intensity.

Teacher Rated School Ethos and Student Reported Bullying-A Multilevel Study of Upper Secondary Schools in Stockholm, Sweden.

PubMed

Modin, Bitte; Låftman, Sara B; Östberg, Viveca

2017-12-13

School ethos refers to the school leadership's purposive efforts to shape and direct the attitudes, values and behaviors needed in order to promote an active learning environment and to prevent the emergence of undesirable behaviors by creating shared meaning and common goals for the school. The aim of this study was to examine how teacher rated aspects of school ethos are linked with manifestations of bullying among 11th grade students. Five teacher-rated sub-dimensions of school ethos (staff stability, teacher morale, structure-order, student focus, and academic atmosphere) were examined in relation to student-reported perpetration of and exposure to traditional school bullying and cyberbullying. The data material combines student and teacher information from two separate data collections performed in 2016, comprising teachers and students in 58 upper secondary schools in Stockholm. Analyses showed that bullying was associated with all but one of the five sub-dimensions of school ethos, namely structure and order for dealing with bullying behaviors at the school. Results are discussed in light of this counter-intuitive finding. Our findings nevertheless lend support to the idea that the social organization of schools, as reflected in their teacher-rated ethos, can affect individual students' attitudes in a way that prevents the emergence of bullying behavior among students.

Advantages of synchrotron radiation circular dichroism spectroscopy to study intrinsically disordered proteins.

PubMed

Kumagai, Patricia S; DeMarco, Ricardo; Lopes, Jose L S

2017-10-01

The unordered secondary structural content of an intrinsically disordered protein (IDP) is susceptible to conformational changes induced by many different external factors, such as the presence of organic solvents, removal of water, changes in temperature, binding to partner molecules, and interaction with lipids and/or other ligands. In order to characterize the high-flexibility nature of an IDP, circular dichroism (CD) spectroscopy is a particularly useful method due to its capability of monitoring both subtle and remarkable changes in different environments, relative ease in obtaining measurements, the small amount of sample required, and the capability for sample recovery (sample not damaged) and others. Using synchrotron radiation as the light source for CD spectroscopy represents the state-of-the-art version of this technique with feasibility of accessing the lower wavelength UV region, and therefore presenting a series of advantages over conventional circular dichroism (cCD) to monitor a protein conformational behavior, check protein stability, detect ligand binding, and many others. In this paper, we have performed a comparative study using cCD and SRCD methods for investigating the secondary structure and the conformational behavior of natively unfolded proteins: MEG-14 and soybean trypsin inhibitor. We show that the SRCD technique greatly improves the analysis and accuracy of the studies on the conformations of IDPs.

Biological Effects of Particles with Very High Energy Deposition on Mammalian Cells Utilizing the Brookhaven Tandem Van de Graaff Accelerator

NASA Technical Reports Server (NTRS)

Saha, Janapriya; Cucinotta, Francis A.; Wang, Minli

2013-01-01

High LET radiation from GCR (Galactic Cosmic Rays) consisting mainly of high charge and energy (HZE) nuclei and secondary protons and neutrons, and secondaries from protons in SPE (Solar Particle Event) pose a major health risk to astronauts due to induction of DNA damage and oxidative stress. Experiments with high energy particles mimicking the space environment for estimation of radiation risk are being performed at NASA Space Radiation Laboratory at BNL. Experiments with low energy particles comparing to high energy particles of similar LET are of interest for investigation of the role of track structure on biological effects. For this purpose, we report results utilizing the Tandem Van de Graaff accelerator at BNL. The primary objective of our studies is to elucidate the influence of high vs low energy deposition on track structure, delta ray contribution and resulting biological responses. These low energy ions are of special relevance as these energies may occur following absorption through the spacecraft and shielding materials in human tissues and nuclear fragments produced in tissues by high energy protons and neutrons. This study will help to verify the efficiency of these low energy particles and better understand how various cell types respond to them.

Determination of Secondary School Students' Cognitive Structure, and Misconception in Ecological Concepts through Word Association Test

ERIC Educational Resources Information Center

Yücel, Elif Özata; Özkan, Mulis

2015-01-01

In this study, we determined cognitive structures and misconceptions about basic ecological concepts by using "word association" tests on secondary school students, age between 12-14 years. Eighty-nine students participated in this study. Before WAT was generated, basic ecological concepts that take place in the secondary science…

Differences in sociocultural environment perceptions associated with gender in science classrooms

NASA Astrophysics Data System (ADS)

Jegede, Olugbemiro J.; Akinsola Okebukola, Peter

An amount-of-learning outcome variable has been attributed to the environment in which teaching and learning are conducted. Studies carried out so far have, however, not focused on the sociocultural aspect of the classroom environment, which has been theorized to have potential influence on students' learning. The intent of this study was to examine the influence of five aspects of the sociocultural environment in science classes with particular reference to how these are perceived by boys and girls. The 30-item Socio-Cultural Environment Scale (SCES) developed by Jegede and Okebukola (1988) was used to collect data from 707 Nigerian secondary school students in Classes Four and Five (Grades 10 and 11, respectively). Authoritarianism, goal structure, African worldview, societal expectation, and sacredness of science were the five subscales studied. Sex differences were recorded in the societal expectation subscale. Most of the female subjects are of the opinion that society has a negative or low regard for their ability to do science and this has an effect on their motivation to undertake science-based careers. The reverse is true for boys. This perception is in agreement with the literature on sex differences in science education and highlights the social pressure that brings about subject preferences. The implications of these findings for science teaching and further research are highlighted.

Perceptions by medical students of their educational environment for obstetrics and gynaecology in metropolitan and rural teaching sites.

PubMed

Carmody, Dianne F; Jacques, Angela; Denz-Penhey, Harriet; Puddey, Ian; Newnham, John P

2009-12-01

Medical student education in Western Australia is expanding to secondary level metropolitan hospitals and rural sites to accommodate workforce demands and increasing medical student numbers. To determine if students' perceptions of the teaching environment for obstetrics and gynaecology differ between tertiary, secondary level metropolitan hospitals and rural sites, and to determine if students' perceptions of their learning environment are associated with improved academic performance. An evaluation was conducted of medical students' perceptions of their learning environment during an obstetrics and gynaecology program at a variety of sites across metropolitan and rural Western Australia. The evaluation was based on the Dundee Ready Education Environmental Measure (DREEM) questionnaire. There were no significant differences in students' perceptions of their learning environment between the tertiary hospital, combined programs involving a tertiary and secondary metropolitan hospital, rural sites with a population of more than 25,000 and rural sites with a population less than 25,000 people. Perceptions were similar in male and female students. The overall mean score for all perceptions of the learning environment in obstetrics and gynaecology were in the range considered to be favorable. Higher scores of perceptions of the learning environment were associated positively with the measures of academic achievement in the clinical, but not written, examination. Medical students' perceptions of their learning environment in obstetrics and gynaecology were not influenced by the geographical site of delivery or their gender but were positively related to higher academic achievement. Providing appropriate academic and clinical support systems have been put in place the education of medical students can be extended outside major hospitals and into outer metropolitan and rural communities without any apparent reduction in perceptions of the quality of their learning environment.

Characterization and visualization of RNA secondary structure Boltzmann ensemble via information theory.

PubMed

Lin, Luan; McKerrow, Wilson H; Richards, Bryce; Phonsom, Chukiat; Lawrence, Charles E

2018-03-05

The nearest neighbor model and associated dynamic programming algorithms allow for the efficient estimation of the RNA secondary structure Boltzmann ensemble. However because a given RNA secondary structure only contains a fraction of the possible helices that could form from a given sequence, the Boltzmann ensemble is multimodal. Several methods exist for clustering structures and finding those modes. However less focus is given to exploring the underlying reasons for this multimodality: the presence of conflicting basepairs. Information theory, or more specifically mutual information, provides a method to identify those basepairs that are key to the secondary structure. To this end we find most informative basepairs and visualize the effect of these basepairs on the secondary structure. Knowing whether a most informative basepair is present tells us not only the status of the particular pair but also provides a large amount of information about which other pairs are present or not present. We find that a few basepairs account for a large amount of the structural uncertainty. The identification of these pairs indicates small changes to sequence or stability that will have a large effect on structure. We provide a novel algorithm that uses mutual information to identify the key basepairs that lead to a multimodal Boltzmann distribution. We then visualize the effect of these pairs on the overall Boltzmann ensemble.

A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments

PubMed Central

Cao, Chen; Wang, Guishen; Liu, An; Xu, Shutan; Wang, Lincong; Zou, Shuxue

2016-01-01

The assignment of secondary structure elements in proteins is a key step in the analysis of their structures and functions. We have developed an algorithm, SACF (secondary structure assignment based on Cα fragments), for secondary structure element (SSE) assignment based on the alignment of Cα backbone fragments with central poses derived by clustering known SSE fragments. The assignment algorithm consists of three steps: First, the outlier fragments on known SSEs are detected. Next, the remaining fragments are clustered to obtain the central fragments for each cluster. Finally, the central fragments are used as a template to make assignments. Following a large-scale comparison of 11 secondary structure assignment methods, SACF, KAKSI and PROSS are found to have similar agreement with DSSP, while PCASSO agrees with DSSP best. SACF and PCASSO show preference to reducing residues in N and C cap regions, whereas KAKSI, P-SEA and SEGNO tend to add residues to the terminals when DSSP assignment is taken as standard. Moreover, our algorithm is able to assign subtle helices (310-helix, π-helix and left-handed helix) and make uniform assignments, as well as to detect rare SSEs in β-sheets or long helices as outlier fragments from other programs. The structural uniformity should be useful for protein structure classification and prediction, while outlier fragments underlie the structure–function relationship. PMID:26978354

Secondary electron imaging of monolayer materials inside a transmission electron microscope

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

Cretu, Ovidiu, E-mail: cretu.ovidiu@nims.go.jp; Lin, Yung-Chang; Suenaga, Kazutomo

2015-08-10

A scanning transmission electron microscope equipped with a backscattered and secondary electron detector is shown capable to image graphene and hexagonal boron nitride monolayers. Secondary electron contrasts of the two lightest monolayer materials are clearly distinguished from the vacuum level. A signal difference between these two materials is attributed to electronic structure differences, which will influence the escape probabilities of the secondary electrons. Our results show that the secondary electron signal can be used to distinguish between the electronic structures of materials with atomic layer sensitivity, enhancing its applicability as a complementary signal in the analytical microscope.

Computing the Partition Function for Kinetically Trapped RNA Secondary Structures

PubMed Central

Lorenz, William A.; Clote, Peter

2011-01-01

An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely accepted Turner nearest neighbor model. Locally optimal structures form kinetic traps, since any evolution away from a locally optimal structure must involve energetically unfavorable folding steps. Here, we present a novel, efficient algorithm to compute the partition function over all locally optimal secondary structures of a given RNA sequence. Our software, RNAlocopt runs in time and space. Additionally, RNAlocopt samples a user-specified number of structures from the Boltzmann subensemble of all locally optimal structures. We apply RNAlocopt to show that (1) the number of locally optimal structures is far fewer than the total number of structures – indeed, the number of locally optimal structures approximately equal to the square root of the number of all structures, (2) the structural diversity of this subensemble may be either similar to or quite different from the structural diversity of the entire Boltzmann ensemble, a situation that depends on the type of input RNA, (3) the (modified) maximum expected accuracy structure, computed by taking into account base pairing frequencies of locally optimal structures, is a more accurate prediction of the native structure than other current thermodynamics-based methods. The software RNAlocopt constitutes a technical breakthrough in our study of the folding landscape for RNA secondary structures. For the first time, locally optimal structures (kinetic traps in the Turner energy model) can be rapidly generated for long RNA sequences, previously impossible with methods that involved exhaustive enumeration. Use of locally optimal structure leads to state-of-the-art secondary structure prediction, as benchmarked against methods involving the computation of minimum free energy and of maximum expected accuracy. Web server and source code available at http://bioinformatics.bc.edu/clotelab/RNAlocopt/. PMID:21297972

Historical changes in the structure and functioning of the benthic community in the lagoon of Venice

NASA Astrophysics Data System (ADS)

Pranovi, Fabio; Da Ponte, Filippo; Torricelli, Patrizia

2008-03-01

One of the main challenges in environmental management is how to manage the dynamics of natural environments. In this context, having information about historical changes of the structure of the biological communities could represent a useful tool to improve management strategies, contributing to refine the policy objectives, since it gives reference states with which to compare the present. The Venice lagoon represents an interesting case study, since it is a highly dynamic, but sensitive, environment which requires the adoption of prudent management. In its recent history the lagoon ecosystem has been exposed to different kinds of disturbance, from the discharge of pollutants and nutrients, to the invasion of alien species and the exploitation of its biological resources by using highly impacting fishing gears. The analysis of available data about the macro-benthic community, from 1935 to 2004, allows the description of changes of the community structure over almost 70 years, showing a sharp decrease in its diversity. In order to obtain information about its functioning, it is necessary to know how these changes have affected processes at the community and system level. In shallow water ecosystems, as the control is mainly due to the benthic compartment, variations in the structure of the benthic community can induce modifications in processes at different hierarchical levels. The trophic structure analysis has revealed major changes during the period; from a well-assorted structure in 1935, to an herbivore-detritivore dominated one in the 1990s, and finally to a filter feeder dominated structure during the last decade. This has produced variations in the secondary production and it has induced modifications in the type of the ecosystem control. These changes are discussed in the light of the dynamics of the main driving forces.

Tools for Evaluating Fault Detection and Diagnostic Methods for HVAC Secondary Systems

NASA Astrophysics Data System (ADS)

Pourarian, Shokouh

Although modern buildings are using increasingly sophisticated energy management and control systems that have tremendous control and monitoring capabilities, building systems routinely fail to perform as designed. More advanced building control, operation, and automated fault detection and diagnosis (AFDD) technologies are needed to achieve the goal of net-zero energy commercial buildings. Much effort has been devoted to develop such technologies for primary heating ventilating and air conditioning (HVAC) systems, and some secondary systems. However, secondary systems, such as fan coil units and dual duct systems, although widely used in commercial, industrial, and multifamily residential buildings, have received very little attention. This research study aims at developing tools that could provide simulation capabilities to develop and evaluate advanced control, operation, and AFDD technologies for these less studied secondary systems. In this study, HVACSIM+ is selected as the simulation environment. Besides developing dynamic models for the above-mentioned secondary systems, two other issues related to the HVACSIM+ environment are also investigated. One issue is the nonlinear equation solver used in HVACSIM+ (Powell's Hybrid method in subroutine SNSQ). It has been found from several previous research projects (ASRHAE RP 825 and 1312) that SNSQ is especially unstable at the beginning of a simulation and sometimes unable to converge to a solution. Another issue is related to the zone model in the HVACSIM+ library of components. Dynamic simulation of secondary HVAC systems unavoidably requires an interacting zone model which is systematically and dynamically interacting with building surrounding. Therefore, the accuracy and reliability of the building zone model affects operational data generated by the developed dynamic tool to predict HVAC secondary systems function. The available model does not simulate the impact of direct solar radiation that enters a zone through glazing and the study of zone model is conducted in this direction to modify the existing zone model. In this research project, the following tasks are completed and summarized in this report: 1. Develop dynamic simulation models in the HVACSIM+ environment for common fan coil unit and dual duct system configurations. The developed simulation models are able to produce both fault-free and faulty operational data under a wide variety of faults and severity levels for advanced control, operation, and AFDD technology development and evaluation purposes; 2. Develop a model structure, which includes the grouping of blocks and superblocks, treatment of state variables, initial and boundary conditions, and selection of equation solver, that can simulate a dual duct system efficiently with satisfactory stability; 3. Design and conduct a comprehensive and systematic validation procedure using collected experimental data to validate the developed simulation models under both fault-free and faulty operational conditions; 4. Conduct a numerical study to compare two solution techniques: Powell's Hybrid (PH) and Levenberg-Marquardt (LM) in terms of their robustness and accuracy. 5. Modification of the thermal state of the existing building zone model in HVACSIM+ library of component. This component is revised to consider the transmitted heat through glazing as a heat source for transient building zone load prediction In this report, literature, including existing HVAC dynamic modeling environment and models, HVAC model validation methodologies, and fault modeling and validation methodologies, are reviewed. The overall methodologies used for fault free and fault model development and validation are introduced. Detailed model development and validation results for the two secondary systems, i.e., fan coil unit and dual duct system are summarized. Experimental data mostly from the Iowa Energy Center Energy Resource Station are used to validate the models developed in this project. Satisfactory model performance in both fault free and fault simulation studies is observed for all studied systems.

A 'periodic table' for protein structures.

PubMed

Taylor, William R

2002-04-11

Current structural genomics programs aim systematically to determine the structures of all proteins coded in both human and other genomes, providing a complete picture of the number and variety of protein structures that exist. In the past, estimates have been made on the basis of the incomplete sample of structures currently known. These estimates have varied greatly (between 1,000 and 10,000; see for example refs 1 and 2), partly because of limited sample size but also owing to the difficulties of distinguishing one structure from another. This distinction is usually topological, based on the fold of the protein; however, in strict topological terms (neglecting to consider intra-chain cross-links), protein chains are open strings and hence are all identical. To avoid this trivial result, topologies are determined by considering secondary links in the form of intra-chain hydrogen bonds (secondary structure) and tertiary links formed by the packing of secondary structures. However, small additions to or loss of structure can make large changes to these perceived topologies and such subjective solutions are neither robust nor amenable to automation. Here I formalize both secondary and tertiary links to allow the rigorous and automatic definition of protein topology.

FTIR study of secondary structure of bovine serum albumin and ovalbumin

NASA Astrophysics Data System (ADS)

Abrosimova, K. V.; Shulenina, O. V.; Paston, S. V.

2016-11-01

Proteins structure is the critical factor for their functioning. Fourier transform infrared spectroscopy provides a possibility to obtain information about secondary structure of proteins in different states and also in a whole biological samples. Infrared spectra of egg white from the untreated and hard-boiled hen's egg, and also of chicken ovalbumin and bovine serum albumin in lyophilic form and in aqueous solution were studied. Lyophilization of investigated globular proteins is accompanied by the decrease of a-helix structures and the increase in amount of intermolecular β-sheets. Analysis of infrared spectrum of egg white allowed to make an estimation of OVA secondary structure and to observe α-to-β structural transformation as a result of the heat denaturation.

Challenging Heteronormativity: Creating a Safe and Inclusive Environment for LGBTQ Students

ERIC Educational Resources Information Center

Steck, Andy K.; Perry, David

2018-01-01

Lesbian, gay, bisexual, transgender, and queer/questioning (LGBTQ) youth face hostile and exclusionary learning environments. A qualitative phenomenographic method involving semistructured interviews of seven secondary school administrators was conducted to identify perceptions of experiences creating a safe and inclusive environment for students…

Chemical-biogeographic survey of secondary metabolism in soil.

PubMed

Charlop-Powers, Zachary; Owen, Jeremy G; Reddy, Boojala Vijay B; Ternei, Melinda A; Brady, Sean F

2014-03-11

In this study, we compare biosynthetic gene richness and diversity of 96 soil microbiomes from diverse environments found throughout the southwestern and northeastern regions of the United States. The 454-pyroseqencing of nonribosomal peptide adenylation (AD) and polyketide ketosynthase (KS) domain fragments amplified from these microbiomes provide a means to evaluate the variation of secondary metabolite biosynthetic diversity in different soil environments. Through soil composition and AD- and KS-amplicon richness analysis, we identify soil types with elevated biosynthetic potential. In general, arid soils show the richest observed biosynthetic diversity, whereas brackish sediments and pine forest soils show the least. By mapping individual environmental amplicon sequences to sequences derived from functionally characterized biosynthetic gene clusters, we identified conserved soil type-specific secondary metabolome enrichment patterns despite significant sample-to-sample sequence variation. These data are used to create chemical biogeographic distribution maps for biomedically valuable families of natural products in the environment that should prove useful for directing the discovery of bioactive natural products in the future.

The radiation environment on the Moon from galactic cosmic rays in a lunar habitat.

PubMed

Jia, Y; Lin, Z W

2010-02-01

We calculated how the radiation environment in a habitat on the surface of the Moon would have depended on the thickness of the habitat in the 1977 galactic cosmic-ray environment. The Geant4 Monte Carlo transport code was used, and a hemispherical dome made of lunar regolith was used to simulate the lunar habitat. We investigated the effective dose from primary and secondary particles including nuclei from protons up to nickel, neutrons, charged pions, photons, electrons and positrons. The total effective dose showed a strong decrease with the thickness of the habitat dome. However, the effective dose values from secondary neutrons, charged pions, photons, electrons and positrons all showed a strong increase followed by a gradual decrease with the habitat thickness. The fraction of the summed effective dose from these secondary particles in the total effective dose increased with the habitat thickness, from approximately 5% for the no-habitat case to about 47% for the habitat with an areal thickness of 100 g/cm(2).

Electromagnetic interference-aware transmission scheduling and power control for dynamic wireless access in hospital environments.

PubMed

Phunchongharn, Phond; Hossain, Ekram; Camorlinga, Sergio

2011-11-01

We study the multiple access problem for e-Health applications (referred to as secondary users) coexisting with medical devices (referred to as primary or protected users) in a hospital environment. In particular, we focus on transmission scheduling and power control of secondary users in multiple spatial reuse time-division multiple access (STDMA) networks. The objective is to maximize the spectrum utilization of secondary users and minimize their power consumption subject to the electromagnetic interference (EMI) constraints for active and passive medical devices and minimum throughput guarantee for secondary users. The multiple access problem is formulated as a dual objective optimization problem which is shown to be NP-complete. We propose a joint scheduling and power control algorithm based on a greedy approach to solve the problem with much lower computational complexity. To this end, an enhanced greedy algorithm is proposed to improve the performance of the greedy algorithm by finding the optimal sequence of secondary users for scheduling. Using extensive simulations, the tradeoff in performance in terms of spectrum utilization, energy consumption, and computational complexity is evaluated for both the algorithms.

Accumulation of flavonoids and related compounds in birch induced by UV-B irradiance.

PubMed

Lavola, Anu

1998-01-01

A growth chamber experiment was conducted to examine the effects of UV-B exposure (4.9 kJ m(-2) day(-1) of biologically effective UV-B, 280-320 nm) on shoot growth and secondary metabolite production in Betula pendula (Roth) and B. resinifera (Britt.) seedlings originating from environments in Finland, Germany and Alaska differing in solar UV-B radiation and climate. Neither shoot growth nor the composition of secondary metabolites was affected by UV-B irradiance, but the treatment induced significant changes in the amounts of individual secondary metabolites in leaves. Leaves of seedlings exposed to UV-B radiation contained higher concentrations of several flavonoids, condensed tannins and some hydroxycinnamic acids than leaves of control seedlings that received no UV-B radiation. At the population level, there was considerable variation in secondary metabolite responses to UV-B radiation: among populations, the induced response was most prominent in Alaskan populations, which were adapted to the lowest ambient UV-B radiation environment. I conclude that solar UV-B radiation plays an important role in the formation of secondary chemical characteristics in birch trees.

[Effects of cultivation environments on Dendrobium catenatum].

PubMed

Lin, Yi-Kai; Zhu, Yu-Qiu; Si, Jin-Ping; Qin, Lang; Zhu, Yan; Wu, Ling-Shang; Liu, Jing-Jing

2017-08-01

The study was aimed to clarify the effect of three cultivation environments on the growth and metabolism of Dendrobium catenatum C13 group. There were three different cultivation conditions including rock epiphytic cultivation, pear epiphytic cultivation and pot cultivation. Morphological characteristics and agronomic characters of D. catenatum were observed and measured. Microstructure, contents of polysaccharide and alcohol-soluble extracts were measured by paraffin section method, phenol-sulfuric acid method and hot-dip method, respectively. The result showed that the cultivation environment significantly affected the growth of D. catenatum, the leaves of D. catenatum that cultivated on the rock and pear were sparse and small, the stems were short and purple and the root system was developed. Compare with potted cultivation, D. catenatum from rock epiphytic cultivation and pear epiphytic cultivation showed the following characteristics in the microstructure: the upper epidermis became thicker, the epidermal hair in the epidermis became denser, stomatal showed smaller and denser, the cell wall of exodermis, endoderm and medulla became thicker, the cell of velamen, exodermis, endoderm and medulla were smaller and arranged more closely, but the cultivation environment did not produce specific tissue structure, mainly changed in the structural parameters of size and quantity. The growth environments also influenced contents of polysaccharides and alcohol-soluble extracts. The dontents of polysaccharides and alcohol-soluble extracts in D. catenatum from rock epiphytic were the highest, reached 37.34% and 11.66%, the second was pear epiphytic, both higher than pot cultivation, alcohol-soluble extracts contents in D. catenatum from rock epiphytic are more complex, which shows that rock epiphytic is conducive to the accumulation of secondary metabolites in D. catenatum. Copyright© by the Chinese Pharmaceutical Association.

X-ray absorption and Raman spectroscopy studies of molybdenum environments in borosilicate waste glasses

NASA Astrophysics Data System (ADS)

McKeown, David A.; Gan, Hao; Pegg, Ian L.

2017-05-01

Mo-containing high-level nuclear waste borosilicate glasses were investigated as part of an effort to improve Mo loading while avoiding yellow phase crystallization. Previous work showed that additions of vanadium decrease yellow phase formation and increases Mo solubility. X-ray absorption spectroscopy (XAS) and Raman spectroscopy were used to characterize Mo environments in HLW borosilicate glasses and to investigate possible structural relationships between Mo and V. Mo XAS spectra for the glasses indicate isolated tetrahedral Mo6+O4 with Mo-O distances near 1.75 Å. V XANES indicate tetrahedral V5+O4 as the dominant species. Raman spectra show composition dependent trends, where Mo-O symmetrical stretch mode frequencies (ν1) are sensitive to the mix of alkali and alkaline earth cations, decreasing by up to 10 cm-1 for glasses that change from Li+ to Na+ as the dominant network-modifying species. This indicates that MoO4 tetrahedra are isolated from the borosilicate network and are surrounded, at least partly, by Na+ and Li+. Secondary ν1 frequency effects, with changes up to 7 cm-1, were also observed with increasing V2O5 and MoO3 content. These secondary trends may indicate MoO4-MoO4 and MoO4-VO4 clustering, suggesting that V additions may stabilize Mo in the matrix with respect to yellow phase formation.

The influence of the secondary school setting on the food practices of young teenagers from disadvantaged backgrounds in Scotland.

PubMed

Wills, W; Backett-Milburn, K; Gregory, S; Lawton, J

2005-08-01

In this paper, we explore the secondary school environment as an important context for understanding young teenagers' eating habits and food practices. We draw on data collected during semi-structured interviews with 36 young teenagers (aged 13/14 years) living in disadvantaged circumstances in Scotland. We found that the systems inherent in school had an impact on what, where and when participants ate their lunch. Each school had rules governing use of the school dining hall and participants sometimes chose to leave this environment to buy food outside school premises. Our interviews showed that parents determined how much money young people took to school and, therefore, had some control over their food choices. Participants rarely spoke of giving priority to food and eating during the non-curriculum parts of the school day, preferring to spend time 'hanging out' with friends. Eating with friends was sometimes reported as a cause of anxiety, particularly when participants had concerns about body image, appetite or appearance. We suggest that young teenagers' dislike for queuing for food, their ability to budget for food at school and their desire to maximize time spent with friends influence food choices; therefore, these are issues which have implications for health education and will be of interest to those responsible for school meal provision.

Agricultural legacies in forest environments: tree communities, soil properties, and light availability.

PubMed

Flinn, Kathryn M; Marks, P L

2007-03-01

Temperate deciduous forests across much of Europe and eastern North America reflect legacies of past land use, particularly in the diversity and composition of plant communities. Intense disturbances, such as clearing forests for agriculture, may cause persistent environmental changes that continue to shape vegetation patterns as landscapes recover. We assessed the long-term consequences of agriculture for environmental conditions in central New York forests, including tree community structure and composition, soil physical and chemical properties, and light availability. To isolate the effects of agriculture, we compared 20 adjacent pairs of forests that were never cleared for agriculture (primary forests) and forests that established 85-100 years ago on plowed fields (secondary forests). Tree communities in primary and secondary forests had similar stem density, though secondary forests had 14% greater basal area. Species composition differed dramatically between the two forest types, with primary forests dominated by Acer saccharum and Fagus grandifolia and secondary forests by Acer rubrum and Pinus strobus. Primary and secondary forests showed no consistent differences in soil physical properties or in the principal gradient of soil fertility associated with soil pH. Within stands, however, soil water content and pH were more variable in primary forests. Secondary forest soils had 15% less organic matter, 16% less total carbon, and 29% less extractable phosphorus in the top 10 cm than adjacent primary stands, though the ranges of the forest types mostly overlapped. Understory light availability in primary and secondary forests was similar. These results suggest that, within 100 years, post-agricultural stands have recovered conditions comparable to less disturbed forests in many attributes, including tree size and number, soil physical properties, soil chemical properties associated with pH, and understory light availability. The principal legacies of agriculture that remain in these forests are the reduced levels of soil organic matter, carbon, and phosphorus; the spatial homogenization of soil properties; and the altered species composition of the vegetation.

Crystal Structure and Chemical Composition of a Presolar Silicate from the Queen Elizabeth Range 99177 Meteorite

NASA Technical Reports Server (NTRS)

Nguyen, A. N.; Keller, L. P.; Rahman, Z.; Messenger, S.

2013-01-01

Mineral characterization of presolar silicate grains, the most abundant stardust phase, has provided valuable information about the formation conditions in circumstellar environments and in super-nova (SN) outflows. Spectroscopic observations of dust around evolved stars suggest a majority of amor-phous, Mg-rich olivine grains, but crystalline silicates, most of which are pyroxene, have also been observed [1]. The chemical compositions of hundreds of presolar silicates have been determined by Auger spectroscopy and reveal high Fe contents and nonstoichiometric compositions intermediate to olivine and pyroxene [2-6]. The unexpectedly high Fe contents can partly be attributed to secondary alteration on the meteorite parent bodies, as some grains have Fe isotopic anomalies from their parent stellar source [7]. Only about 35 presolar silicates have been studied for their mineral structures and chemical compositions by transmission electron microscopy (TEM). These grains display a wide range of compositions and structures, including crystalline forsterite, crystalline pyroxene, nanocrystalline grains, and a majority of amorphous nonstoichiometric grains. Most of these grains were identified in the primitive Acfer 094 meteorite. Presolar silicates from this meteorite show a wide range of Fe-contents, suggestive of secondary processing on the meteorite parent body. The CR chondrite QUE 99177 has not suffered as much alteration [8] and displays the highest presolar silicate abundance to date among carbonaceous chondrites [3, 6]. However, no mineralogical studies of presolar silicates from this meteorite have been performed. Here we examine the mineralogy of a presolar silicate from QUE 99177.

Halide salts and their structural properties in presence of secondary amine based molecule: A combined experimental and theoretical analysis

NASA Astrophysics Data System (ADS)

Ghosh, Pritam; Hazra, Abhijit; Ghosh, Meenakshi; Chandra Murmu, Naresh; Banerjee, Priyabrata

2018-04-01

Biologically relevant halide salts and its solution state structural properties are always been significant. In general, exposure of halide salts into polar solution medium results in solvation which in turn separates the cationic and anionic part of the salt. However, the conventional behaviour of salts might alter in presence of any secondary amine based compound, i.e.; moderately strong Lewis acid. In its consequence, to investigate the effect of secondary amine based compound in the salt solution, novel (E)-2-(4-bromobenzylidene)-1-(perfluorophenyl) hydrazine has been synthesized and used as secondary amine source. The secondary amine compound interestingly shows a drastic color change upon exposure to fluoride salts owing to hydrogen bonding interaction. Several experimental methods, e.g.; SCXRD, UV-Vis, FT-IR, ESI-MS and DLS together with modern DFT (i.e.; DFT-D3) have been performed to explore the structural properties of the halide salts upon exposure to secondary amine based compound. The effect of counter cation of the fluoride salt in binding with secondary amine source has also been investigated.

Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations.

PubMed

Goldschmidt, Felix; Regoes, Roland R; Johnson, David R

2017-09-01

Successive range expansions occur within all domains of life, where one population expands first (primary expansion) and one or more secondary populations then follow (secondary expansion). In general, genetic drift reduces diversity during range expansion. However, it is not clear whether the same effect applies during successive range expansion, mainly because the secondary population must expand into space occupied by the primary population. Here we used an experimental microbial model system to show that, in contrast to primary range expansion, successive range expansion promotes local population diversity. Because of mechanical constraints imposed by the presence of the primary population, the secondary population forms fractal-like dendritic structures. This divides the advancing secondary population into many small sub-populations and promotes intermixing between the primary and secondary populations. We further developed a mathematical model to simulate the formation of dendritic structures in the secondary population during succession. By introducing mutations in the primary or dendritic secondary populations, we found that mutations are more likely to accumulate in the dendritic secondary populations. Our results thus show that successive range expansion can promote intermixing over the short term and increase genetic diversity over the long term. Our results therefore have potentially important implications for predicting the ecological processes and evolutionary trajectories of microbial communities.

Stress Producing Conditions in the Secondary Classroom.

ERIC Educational Resources Information Center

Bruner, Anna L.; And Others

Secondary school teachers in the Houston Independent School District were asked for their perceptions of variables that contributed to difficulty of teaching. A 60-item questionnaire included variables from school environment categories: student characteristics, managerial efficiency, instructional program, material resources, teacher personal…

A simple system for the identification of fluorescent dyes capable of reporting differences in secondary structure and hydrophobicity among amyloidogenic protein oligomers

NASA Astrophysics Data System (ADS)

Yates, Emma

2012-02-01

Thioflavin T and Congo Red are fluorescent dyes that are commonly used to identify the presence of amyloid structures, ordered protein aggregates. Despite the ubiquity of their use, little is known about their mechanism of interaction with amyloid fibrils, or whether other dyes, whose photophysics indicate that they may be more responsive to differences in macromolecular secondary structure and hydrophobicity, would be better suited to the identification of pathologically relevant oligomeric species in amyloid diseases. In order to systematically address this question, we have designed a strategy that discretely introduces differences in secondary structure and hydrophobicity amidst otherwise identical polyamino acids. This strategy will enable us to quantify and compare the affinities of Thioflavin T, Congo Red, and other, incompletely explored, fluorescent dyes for different secondary structural elements and hydrophobic motifs. With this information, we will identify dyes that give the most robust and quantitative information about structural differences among the complex population of oligomeric species present along an aggregation pathway between soluble monomers and amyloid fibrils, and correlate the resulting structural information with differential oligomeric toxicity.

Development of a Neutron Spectrometer to Assess Biological Radiation Damage Behind Spacecraft Materials

NASA Technical Reports Server (NTRS)

Maurer, R. H.; Kinnison, J. D.; Roth, D. R.; Miller, J.; Heilbronn, L.; Zeitlin, C.; Singleterry, R.

2001-01-01

Astronauts who spend months and years traveling long distances in spacecraft and working on other planets will be subjected to high energy radiation of galactic and solar origin without the protection of the Earth's thick (one writer has called it buff) atmosphere and magnetic field. The lack of natural protection will allow high energy cosmic ray particles and solar protons to crash directly into relatively thin spacecraft walls and planetary atmospheres producing energetic secondary particles in these collisions. A substantial fraction of these secondaries will be neutrons that carry no electric charge and, consequently, are difficult to detect. At sea level on Earth the remaining neutrons are the result of many generations (approximately 10) of collisions, have very low energies (scientists call them thermal neutrons), and do not penetrate deeply into the human body. They do contribute to the natural background radiation seen by humans on Earth, but much of the dose is only at the surface or skin of the body. In the International Space Station or on the surface of Mars, the secondary neutrons will be the result of only one or two generations of interaction due to the thinner (about a factor of 20 compared to the Earth's atmosphere) walls or atmosphere, have considerably more energy and penetrate deeply into the human body. In addition, neutrons are substantially moderated by hydrogenous material such as water. A significant fraction of the water exists in the astronaut's body. Therefore, the neutron can not only penetrate more deeply into the body, but also be stopped there and deposit all or most of its radiation dose in organs such as the liver, spleen, kidney, etc. We hypothesize that the risk of serious cancers will be increased for the exposed humans. The portable, real time neutron spectrometer being developed by our team will monitor the environment inside spacecraft structures and on planetary surfaces. Activities supported by this grant will evaluate the neutron environment inside several candidate spacecraft materials at accelerator facilities. These experiments will enable engineers to choose the structure materials that minimize the production of secondary neutrons. With the information that the neutron energy spectrometer produces, scientists and doctors will be able to assess the increased risk of cancer and develop countermeasures. The instrument itself will include an alarm system to warn astronauts when high radiation fluxes are occurring so that they can seek shelter immediately.

Effects of temperature and SDS on the structure of beta-glycosidase from the thermophilic archaeon Sulfolobus solfataricus.

PubMed Central

D'auria, S; Barone, R; Rossi, M; Nucci, R; Barone, G; Fessas, D; Bertoli, E; Tanfani, F

1997-01-01

The effects of temperature and SDS on the three-dimensional organization and secondary structure of beta-glycosidase from the thermophilic archaeon Sulfolobus solfataricus were investigated by CD, IR spectroscopy and differential scanning calorimetry. CD spectra in the near UV region showed that the detergent caused a remarkable change in the protein tertiary structure, and far-UV CD analysis revealed only a slight effect on secondary structure. Infrared spectroscopy showed that low concentrations of the detergent (up to 0.02%) induced slight changes in the enzyme secondary structure, whereas high concentrations caused the alpha-helix content to increase at high temperatures and prevented protein aggregation. PMID:9169619

The Role of Carbon in Exotic Crust Formation on Mercury

NASA Technical Reports Server (NTRS)

Vander Kaaden, Kathleen E.; McCubbin, Francis M.

2018-01-01

The terrestrial planets that comprise our inner Solar System, including the Moon, are all rocky bodies that have differentiated into a crust, mantle, and core. Furthermore, all of these bodies have undergone various igneous processes since their time of primary crust formation. These processes have resurfaced each of these bodies, at least in part, resulting in the production of a secondary crust, to which Mercury is no exception. From its first flyby encounter with Mercury on January 14, 2008, the MErcury Surface, Space ENvironment, GEochemistry and Ranging (MESSENGER) spacecraft collected data on the structure, chemical makeup, and density of the planet among other important characteristics. The X-Ray Spectrometer on board MESSENGER measured elevated abundances of sulfur and low abundances of iron, suggesting the planets oxygen fugacity (fO2) is several log10 units below the Iron-Wustite buffer. Similar to the role of other volatiles (e.g. sulfur) on highly reducing planetary bodies, carbon is expected to behave differently in an oxygen starved environment than it does in an oxygen enriched environment (e.g., Earth).

Paracetamol in the environment and its degradation by microorganisms.

PubMed

Wu, Shijin; Zhang, Lili; Chen, Jianmeng

2012-11-01

Paracetamol (4'-hydroxyacetanilide, N-acetyl-p-aminophenol, acetaminophen, and paracetamol) is a widely used over-the-counter analgesic and antipyretic drug. Paracetamol and structural analogs are ubiquitous in the natural environment and easily accumulate in aquatic environment, which have been detected in surface waters, wastewater, and drinking water throughout the world. Paracetamol wastewater is mainly treated by chemical oxidation processes. Although these chemical methods may be available for treating these pollutants, the harsh reaction conditions, the generation of secondary pollutants, and the high operational cost associated with these methods have often made them not a desirable choice. Biodegradation of paracetamol is being considered as an environmentally friendly and low-cost option. The goal of this review is to provide an outline of the current knowledge of biodegradation of paracetamol in the occurrence, degrading bacteria, and proposed metabolic/biodegrading pathways, enzymes and possible intermediates. The comprehensive understanding of the metabolic pathways and enzyme systems involved in the utilization of paracetamol means will be helpful for optimizing and allowing rational design of biodegradation systems for paracetamol-contaminated wastewater.

Longitudinal Effects of Activities, Social Environment, and Psychotropic Medication Use on Behavioral Symptoms of Individuals With Alzheimer's Disease in Nursing Homes.

PubMed

Inventor, Ben R; Farran, Carol J; Paun, Olimpia; Cothran, Fawn; Rajan, Kumar; Swantek, Sandra S; McCann, Judith J

2018-05-08

A secondary data analysis of 25,560 minutes of structured clinical observations from a longitudinal study examined the impact of time-varying background factors, social environment, and psychotropic medication use on behavioral symptoms of nursing home residents with Alzheimer's disease (AD). Data were collected at baseline (N = 177), 12 months (N = 138), and 24 months (N = 111). Mixed-effects regression modeling showed that at 24 months: (a) higher cognitive and physical function and having a private bedroom/bathroom had the most positive influence on resident positive behaviors; (b) use of antipsychotic medications and solitary activities had the most negative influence on resident positive behaviors; (c) higher cognitive function significantly decreased negative behaviors; and (d) care-related activities and total number of psychotropic medications significantly increased negative behaviors. The current study describes risk factors for behavioral disturbances and the impact of activities, social environment, and psychotropic medications on behavioral outcomes in nursing home residents with AD. [Journal of Psychosocial Nursing and Mental Health Services, xx(x), xx-xx.]. Copyright 2018, SLACK Incorporated.

Secondary subharmonic instability of boundary layers with pressure gradient and suction

NASA Technical Reports Server (NTRS)

El-Hady, Nabil M.

1988-01-01

Three-dimensional linear secondary instability is investigated for boundary layers with pressure gradient and suction in the presence of a finite amplitude TS wave. The focus is on principal parametric resonance responsible for a strong growth of subharmonics in a low disturbance environment. Calculations are presented for the effect of pressure gradients and suction on controlling the onset and amplification of the secondary instability.