Identification of GATC- and CCGG-recognizing Type II REases and their putative specificity-determining positions using Scan2S--a novel motif scan algorithm with optional secondary structure constraints.

PubMed

Niv, Masha Y; Skrabanek, Lucy; Roberts, Richard J; Scheraga, Harold A; Weinstein, Harel

2008-05-01

Restriction endonucleases (REases) are DNA-cleaving enzymes that have become indispensable tools in molecular biology. Type II REases are highly divergent in sequence despite their common structural core, function and, in some cases, common specificities towards DNA sequences. This makes it difficult to identify and classify them functionally based on sequence, and has hampered the efforts of specificity-engineering. Here, we define novel REase sequence motifs, which extend beyond the PD-(D/E)XK hallmark, and incorporate secondary structure information. The automated search using these motifs is carried out with a newly developed fast regular expression matching algorithm that accommodates long patterns with optional secondary structure constraints. Using this new tool, named Scan2S, motifs derived from REases with specificity towards GATC- and CGGG-containing DNA sequences successfully identify REases of the same specificity. Notably, some of these sequences are not identified by standard sequence detection tools. The new motifs highlight potential specificity-determining positions that do not fully overlap for the GATC- and the CCGG-recognizing REases and are candidates for specificity re-engineering.

The Purine Bias of Coding Sequences is Determined by Physicochemical Constraints on Proteins.

PubMed

Ponce de Leon, Miguel; de Miranda, Antonio Basilio; Alvarez-Valin, Fernando; Carels, Nicolas

2014-01-01

For this report, we analyzed protein secondary structures in relation to the statistics of three nucleotide codon positions. The purpose of this investigation was to find which properties of the ribosome, tRNA or protein level, could explain the purine bias (Rrr) as it is observed in coding DNA. We found that the Rrr pattern is the consequence of a regularity (the codon structure) resulting from physicochemical constraints on proteins and thermodynamic constraints on ribosomal machinery. The physicochemical constraints on proteins mainly come from the hydropathy and molecular weight (MW) of secondary structures as well as the energy cost of amino acid synthesis. These constraints appear through a network of statistical correlations, such as (i) the cost of amino acid synthesis, which is in favor of a higher level of guanine in the first codon position, (ii) the constructive contribution of hydropathy alternation in proteins, (iii) the spatial organization of secondary structure in proteins according to solvent accessibility, (iv) the spatial organization of secondary structure according to amino acid hydropathy, (v) the statistical correlation of MW with protein secondary structures and their overall hydropathy, (vi) the statistical correlation of thymine in the second codon position with hydropathy and the energy cost of amino acid synthesis, and (vii) the statistical correlation of adenine in the second codon position with amino acid complexity and the MW of secondary protein structures. Amino acid physicochemical properties and functional constraints on proteins constitute a code that is translated into a purine bias within the coding DNA via tRNAs. In that sense, the Rrr pattern within coding DNA is the effect of information transfer on nucleotide composition from protein to DNA by selection according to the codon positions. Thus, coding DNA structure and ribosomal machinery co-evolved to minimize the energy cost of protein coding given the functional constraints on proteins.

Breakfast consumption among Malaysian primary and secondary school children and relationship with body weight status - Findings from the MyBreakfast Study.

PubMed

Tee, E Siong; Nurliyana, Abdul Razak; Norimah, A Karim; Mohamed, Hamid Jan B Jan; Tan, Sue Yee; Appukutty, Mahenderan; Hopkins, Sinead; Thielecke, Frank; Ong, Moi Kim; Ning, Celia; Nasir, Mohd Taib Mohd

2018-01-01

This study aimed to determine the relationship between breakfast consumption and body weight status among primary and secondary school children in Malaysia. This nationwide cross-sectional study involved 5,332 primary school children aged 6 to 12 years and 3,000 secondary school children aged 13 to 17 years. Height and weight were measured and BMI-for-age was determined. Socio-demographic backgrounds, breakfast habits and physical activity levels were assessed using questionnaires. Breakfast frequency was defined as follows: breakfast skippers (ate breakfast 0-2 days/week), irregular breakfast eaters (ate breakfast 3-4 days/week) and regular breakfast eaters (ate breakfast ≥5 days/week). The overall prevalence of breakfast skippers and irregular breakfast eaters was 11.7% and 12.7% respectively. Breakfast skipping was related to age, sex, ethnicity, income and physical activity level. Among primary school boys and secondary school girls, the proportion of overweight/obesity was higher among breakfast skippers (boys: 43.9%, girls: 30.5%) than regular breakfast eaters (boys: 31.2%, girls: 22.7%). Among primary school children, only boys who skipped breakfast had a higher mean BMI-for-age z-score than regular breakfast eaters. Among secondary school boys and girls, BMI-for-age z-score was higher among breakfast skippers than regular breakfast eaters. Compared to regular breakfast eaters, primary school boys who skipped breakfast were 1.71 times (95% CI=1.26-2.32, p=0.001) more likely to be overweight/obese, while the risk was lower in primary school girls (OR=1.36, 95% CI=1.02-1.81, p=0.039) and secondary school girls (OR=1.38, 95% CI=1.01-1.90, p=0.044). Regular breakfast consumption was associated with a healthier body weight status and is a dietary behaviour which should be encouraged.

Attitudes of Secondary Regular School Teachers toward Inclusive Education in New Delhi, India: A Qualitative Study

ERIC Educational Resources Information Center

Bhatnagar, Nisha; Das, Ajay

2014-01-01

This study aimed to identify the attitudes of regular school teachers in Delhi, India, toward the inclusion of students with disabilities. It also explored their views regarding facilitators of inclusive education. Respondents were secondary school teachers working in schools in Delhi that implement inclusive education for students with…

Perceptions of Secondary School Students with Mild Disabilities to the Academic and Social Support Mechanisms Implemented in Regular Classrooms

ERIC Educational Resources Information Center

O'Rourke, John; Houghton, Stephen

2008-01-01

The Student Perceptions of Classroom Support Scale (SPCS), which measures the perceptions of students with mild disabilities of academic and social support mechanisms implemented in regular classrooms, was administered to 60 secondary school-aged students. Data were obtained with reference to curricular, instructional, physical and peer support…

Evolutionary conservation of sequence and secondary structures inCRISPR repeats

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

Kunin, Victor; Sorek, Rotem; Hugenholtz, Philip

Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel class of direct repeats, separated by unique spacer sequences of similar length, that are present in {approx}40% of bacterial and all archaeal genomes analyzed to date. More than 40 gene families, called CRISPR-associated sequences (CAS), appear in conjunction with these repeats and are thought to be involved in the propagation and functioning of CRISPRs. It has been proposed that the CRISPR/CAS system samples, maintains a record of, and inactivates invasive DNA that the cell has encountered, and therefore constitutes a prokaryotic analog of an immune system. Here we analyze CRISPR repeatsmore » identified in 195 microbial genomes and show that they can be organized into multiple clusters based on sequence similarity. All individual repeats in any given cluster were inferred to form characteristic RNA secondary structure, ranging from non-existent to pronounced. Stable secondary structures included G:U base pairs and exhibited multiple compensatory base changes in the stem region, indicating evolutionary conservation and functional importance. We also show that the repeat-based classification corresponds to, and expands upon, a previously reported CAS gene-based classification including specific relationships between CRISPR and CAS subtypes.« less

Detailed Content of the Vietnamese Secondary Curriculum. Intermediate/Secondary Education Series, No. 2. Indochinese Refugee Education Guides.

ERIC Educational Resources Information Center

Center for Applied Linguistics, Arlington, VA.

This guide furnishes a detailed account of the basic characteristics of the Vietnamese "regular" high school curriculum and system. The regular high school is one of the three main kinds of high schools in Vietnam. Knowing the exact content of the subjects that students took in Viet-Nam will help teachers and administrators in placing…

Faraday wave lattice as an elastic metamaterial.

PubMed

Domino, L; Tarpin, M; Patinet, S; Eddi, A

2016-05-01

Metamaterials enable the emergence of novel physical properties due to the existence of an underlying subwavelength structure. Here, we use the Faraday instability to shape the fluid-air interface with a regular pattern. This pattern undergoes an oscillating secondary instability and exhibits spontaneous vibrations that are analogous to transverse elastic waves. By locally forcing these waves, we fully characterize their dispersion relation and show that a Faraday pattern presents an effective shear elasticity. We propose a physical mechanism combining surface tension with the Faraday structured interface that quantitatively predicts the elastic wave phase speed, revealing that the liquid interface behaves as an elastic metamaterial.

34 CFR 643.22 - How does the Secretary evaluate prior experience?

Code of Federal Regulations, 2012 CFR

2012-07-01

... school enrollment of participants. (3) (3 points) Secondary school graduation (regular secondary school diploma). Whether the applicant met or exceeded its objective regarding the graduation of participants... standard number of years. (4) (1.5 points) Secondary school graduation (rigorous secondary school program...

34 CFR 643.22 - How does the Secretary evaluate prior experience?

Code of Federal Regulations, 2013 CFR

2013-07-01

... school enrollment of participants. (3) (3 points) Secondary school graduation (regular secondary school diploma). Whether the applicant met or exceeded its objective regarding the graduation of participants... standard number of years. (4) (1.5 points) Secondary school graduation (rigorous secondary school program...

34 CFR 643.22 - How does the Secretary evaluate prior experience?

Code of Federal Regulations, 2011 CFR

2011-07-01

... school enrollment of participants. (3) (3 points) Secondary school graduation (regular secondary school diploma). Whether the applicant met or exceeded its objective regarding the graduation of participants... standard number of years. (4) (1.5 points) Secondary school graduation (rigorous secondary school program...

34 CFR 643.22 - How does the Secretary evaluate prior experience?

Code of Federal Regulations, 2014 CFR

2014-07-01

... school enrollment of participants. (3) (3 points) Secondary school graduation (regular secondary school diploma). Whether the applicant met or exceeded its objective regarding the graduation of participants... standard number of years. (4) (1.5 points) Secondary school graduation (rigorous secondary school program...

The secondary structure and the thermal unfolding parameters of the S-layer protein from Lactobacillus salivarius.

PubMed

Lighezan, Liliana; Georgieva, Ralitsa; Neagu, Adrian

2016-09-01

Surface layer (S-layer) proteins have been identified in the cell envelope of many organisms, such as bacteria and archaea. They self-assemble, forming monomolecular crystalline arrays. Isolated S-layer proteins are able to recrystallize into regular lattices, which proved useful in biotechnology. Here we investigate the structure and thermal unfolding of the S-layer protein isolated from Lactobacillus salivarius 16 strain of human origin. Using circular dichroism (CD) spectroscopy, and the software CDSSTR from DICHROWEB, CONTINLL from CDPro, as well as CDNN, we assess the fractions of the protein's secondary structural elements at temperatures ranging between 10 and 90 °C, and predict the tertiary class of the protein. To study the thermal unfolding of the protein, we analyze the temperature dependence of the CD signal in the far- and near-UV domains. Fitting the experimental data by two- and three-state models of thermal unfolding, we infer the midpoint temperatures, the temperature dependence of the changes in Gibbs free energy, enthalpy, and entropy of the unfolding transitions in standard conditions, and the temperature dependence of the equilibrium constant. We also estimate the changes in heat capacity at constant pressure in standard conditions. The results indicate that the thermal unfolding of the S-layer protein from L. salivarius is highly cooperative, since changes in the secondary and tertiary structures occur simultaneously. The thermodynamic analysis predicts a "cold" transition, at about -3 °C, of both the secondary and tertiary structures. Our findings may be important for the use of S-layer proteins in biotechnology and in biomedical applications.

Noise and Stress in Primary and Secondary School Children: Noise Reduction and Increased Concentration Ability through a Short but Regular Exercise and Relaxation Program

ERIC Educational Resources Information Center

Norlander, Torsten; Moas, Leif; Archer, Trevor

2005-01-01

The present study examined whether a short but regularly used program of relaxation, applied to Primary and Secondary school children, could (a) reduce noise levels (in decibels), (b) reduce pupils' experienced stress levels, and (c) increase the pupils' ability to concentrate, as measured by teachers' estimates. Noise levels in 5 classrooms (84…

Who is where? Characteristics of deaf and hard-of-hearing students in regular and special schools.

PubMed

Shaver, Debra M; Marschark, Marc; Newman, Lynn; Marder, Camille

2014-04-01

To address the needs and abilities of deaf and hard-of-hearing (DHH) students in different educational settings, it is important to understand who is in which setting. A secondary analysis of the National Longitudinal Transition Study 2 database was conducted to examine differences in the characteristics of students who attended special schools, such as schools for the deaf, and those who attended regular schools serving a wide variety of students, such as neighborhood, alternative, and charter schools. The study included a nationally (U.S.) representative sample of about 870 DHH secondary school students. Findings from parent interviews and surveys revealed that students who attended only special secondary schools had greater levels of hearing loss, were more likely to use sign language, had more trouble speaking and conversing with others, and were more likely to have low functional mental scores than students who had attended only regular secondary schools. There were no differences in the presence of additional disabilities or cochlear implants between students in the different settings. In many ways, student characteristics did not vary by school type, suggesting that both types of secondary schools serve students with a wide range of needs and abilities.

Impact of pollutants on fish collected from different parts of Shatt Al-Arab River: a histopathological study.

PubMed

Yasser, Amaal Gh; Naser, Murtada D

2011-10-01

In this study, a total of 120 fish specimens of common carp (Cyprinus carpio), were caught at four different stations in Shatt Al-Arab (Hareer, Garmat Ali, Al-Maqal and Abual-Khasib). The histological changes in the gills of fish were detected microscopically. Results show that the Shatt Al-Arab is polluted by some different sources of pollutants including power stations, paper industry, oil refineries, petrochemical industry, chemical fertilizer companies and the sewage system and overfishing and the application of pesticides. As a result of these analyses, histopathological changes in the gills of fish specimens, such as hyperplasia, loss of regular shape of secondary lamellae, separation of lamellar epithelium, clavate structure, atrophy of secondary gills lamellae, necrosis, dilation of lamellar capillaries, loss of secondary lamellae, fusion of secondary lamellae, edema, proliferation of cartilage in primary lamellae and curving of primary lamellae, were observed. The histopathological changes in fish gill samples from the Hareer region were much more prevalent than samples caught from other stations.

Stickiness in Hamiltonian systems: From sharply divided to hierarchical phase space

NASA Astrophysics Data System (ADS)

Altmann, Eduardo G.; Motter, Adilson E.; Kantz, Holger

2006-02-01

We investigate the dynamics of chaotic trajectories in simple yet physically important Hamiltonian systems with nonhierarchical borders between regular and chaotic regions with positive measures. We show that the stickiness to the border of the regular regions in systems with such a sharply divided phase space occurs through one-parameter families of marginally unstable periodic orbits and is characterized by an exponent γ=2 for the asymptotic power-law decay of the distribution of recurrence times. Generic perturbations lead to systems with hierarchical phase space, where the stickiness is apparently enhanced due to the presence of infinitely many regular islands and Cantori. In this case, we show that the distribution of recurrence times can be composed of a sum of exponentials or a sum of power laws, depending on the relative contribution of the primary and secondary structures of the hierarchy. Numerical verification of our main results are provided for area-preserving maps, mushroom billiards, and the newly defined magnetic mushroom billiards.

Regularities in Low-Temperature Phosphatization of Silicates

NASA Astrophysics Data System (ADS)

Savenko, A. V.

2018-01-01

The regularities in low-temperature phosphatization of silicates are defined from long-term experiments on the interaction between different silicate minerals and phosphate-bearing solutions in a wide range of medium acidity. It is shown that the parameters of the reaction of phosphatization of hornblende, orthoclase, and labradorite have the same values as for clayey minerals (kaolinite and montmorillonite). This effect may appear, if phosphotization proceeds, not after silicate minerals with a different structure and composition, but after a secondary silicate phase formed upon interaction between silicates and water and stable in a certain pH range. Variation in the parameters of the reaction of phosphatization at pH ≈ 1.8 is due to the stability of the silicate phase different from that at higher pH values.

The effect of dose reduction on the detection of anatomical structures on panoramic radiographs.

PubMed

Kaeppler, G; Dietz, K; Reinert, S

2006-07-01

The aim was to evaluate the effect of dose reduction on diagnostic accuracy using different screen-film combinations and digital techniques for panoramic radiography. Five observers assessed 201 pairs of panoramic radiographs (a total of 402 panoramic radiographs) taken with the Orthophos Plus (Sirona, Bensheim, Germany), for visualization of 11 anatomical structures on each side, using a 3-point scale -1, 0 and 1. Two radiographs of each patient were taken at two different times (conventional setting and setting with decreased dose, done by increasing tube potential settings or halving tube current). To compare the dose at different tube potential settings dose-length product was measured at the secondary collimator. Films with medium and regular intensifying screens (high and low tube potential settings) and storage phosphor plates (low tube potential setting, tube current setting equivalent to regular intensifying screen and halved) were compared. The five observers made 27 610 assessments. Intrarater agreement was expressed by Cohen's kappa coefficient. The results demonstrated an equivalence of regular screens (low tube potential setting) and medium screens (high and low tube potential settings). A significant difference existed between medium screens (low tube potential setting, mean score 0.92) and the group of regular film-screen combinations at high tube potential settings (mean score 0.89) and between all film-screen combinations and the digital system irrespective of exposure (mean score below 0.82). There were no significant differences between medium and regular screens (mean score 0.88 to 0.92) for assessment of the periodontal ligament space, but there was a significant difference compared with the digital system (mean score below 0.76). The kappa coefficient for intrarater agreement was moderate (0.55). New regular intensifying screens can replace medium screens at low tube potential settings. Digital panoramic radiographs should be taken at low tube potential levels with an exposure equivalent at least to a regular intensifying screen.

Apodized coupled resonator waveguides.

PubMed

Capmany, J; Muñoz, P; Domenech, J D; Muriel, M A

2007-08-06

In this paper we propose analyse the apodisation or windowing of the coupling coefficients in the unit cells of coupled resonator waveguide devices (CROWs) as a means to reduce the level of secondary sidelobes in the bandpass characteristic of their transfer functions. This technique is regularly employed in the design of digital filters and has been applied as well in the design of other photonic devices such as corrugated waveguide filters and fiber Bragg gratings. The apodisation of both Type-I and Type-II structures is discussed for several windowing functions.

[Dominant structural and functional adaptations of distant chemosensory systems in phylogenesis of Gastropoda].

PubMed

Zaĭtseva, O V

2000-08-01

The invasion of land by gastropods independent and repeated in the course of their evolution, was shown to be accompanied by appearance of organisationally similar olfactory tentacular organs and special integrative centres. The majority of primary and secondary water gastropods in different phylogenetic groups had a different, more primitive organisation of the tentacular sensory system as compared to the terrestrial species. Regularities of the phylogenetic adaptations of mollusks to the habitat media and lifestyle are discussed.

Integration of QUARK and I-TASSER for ab initio protein structure prediction in CASP11

PubMed Central

Zhang, Wenxuan; Yang, Jianyi; He, Baoji; Walker, Sara Elizabeth; Zhang, Hongjiu; Govindarajoo, Brandon; Virtanen, Jouko; Xue, Zhidong; Shen, Hong-Bin; Zhang, Yang

2015-01-01

We tested two pipelines developed for template-free protein structure prediction in the CASP11 experiment. First, the QUARK pipeline constructs structure models by reassembling fragments of continuously distributed lengths excised from unrelated proteins. Five free-modeling (FM) targets have the model successfully constructed by QUARK with a TM-score above 0.4, including the first model of T0837-D1, which has a TM-score=0.736 and RMSD=2.9 Å to the native. Detailed analysis showed that the success is partly attributed to the high-resolution contact map prediction derived from fragment-based distance-profiles, which are mainly located between regular secondary structure elements and loops/turns and help guide the orientation of secondary structure assembly. In the Zhang-Server pipeline, weakly scoring threading templates are re-ordered by the structural similarity to the ab initio folding models, which are then reassembled by I-TASSER based structure assembly simulations; 60% more domains with length up to 204 residues, compared to the QUARK pipeline, were successfully modeled by the I-TASSER pipeline with a TM-score above 0.4. The robustness of the I-TASSER pipeline can stem from the composite fragment-assembly simulations that combine structures from both ab initio folding and threading template refinements. Despite the promising cases, challenges still exist in long-range beta-strand folding, domain parsing, and the uncertainty of secondary structure prediction; the latter of which was found to affect nearly all aspects of FM structure predictions, from fragment identification, target classification, structure assembly, to final model selection. Significant efforts are needed to solve these problems before real progress on FM could be made. PMID:26370505

Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11.

PubMed

Zhang, Wenxuan; Yang, Jianyi; He, Baoji; Walker, Sara Elizabeth; Zhang, Hongjiu; Govindarajoo, Brandon; Virtanen, Jouko; Xue, Zhidong; Shen, Hong-Bin; Zhang, Yang

2016-09-01

We tested two pipelines developed for template-free protein structure prediction in the CASP11 experiment. First, the QUARK pipeline constructs structure models by reassembling fragments of continuously distributed lengths excised from unrelated proteins. Five free-modeling (FM) targets have the model successfully constructed by QUARK with a TM-score above 0.4, including the first model of T0837-D1, which has a TM-score = 0.736 and RMSD = 2.9 Å to the native. Detailed analysis showed that the success is partly attributed to the high-resolution contact map prediction derived from fragment-based distance-profiles, which are mainly located between regular secondary structure elements and loops/turns and help guide the orientation of secondary structure assembly. In the Zhang-Server pipeline, weakly scoring threading templates are re-ordered by the structural similarity to the ab initio folding models, which are then reassembled by I-TASSER based structure assembly simulations; 60% more domains with length up to 204 residues, compared to the QUARK pipeline, were successfully modeled by the I-TASSER pipeline with a TM-score above 0.4. The robustness of the I-TASSER pipeline can stem from the composite fragment-assembly simulations that combine structures from both ab initio folding and threading template refinements. Despite the promising cases, challenges still exist in long-range beta-strand folding, domain parsing, and the uncertainty of secondary structure prediction; the latter of which was found to affect nearly all aspects of FM structure predictions, from fragment identification, target classification, structure assembly, to final model selection. Significant efforts are needed to solve these problems before real progress on FM could be made. Proteins 2016; 84(Suppl 1):76-86. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Defining the loop structures in proteins based on composite β-turn mimics.

PubMed

Dhar, Jesmita; Chakrabarti, Pinak

2015-06-01

Asx- and ω-turns are β-turn mimics, which replace the conventional main-chain hydrogen bonds seen in the latter by those involving the side chains, and both involve three residues. In this paper we analyzed the cases where these turns occur together--side by side, with or without any gap, overlapping and in any order. These composite turns (of length 3-15 residues), occurring at ∼1 per 100 residues, may constitute the full length of many loops, and when the residues in the two component turns overlap or are adjacent to each other, the composite may take well-defined shape. It is thus possible for non-regular regions in protein structure to form local structural motifs, akin to the regular geometrical features exhibited by secondary structures. Composites having the order ω-turns followed by Asx-turns can constitute N-terminal helix capping motif. Ternary composite turns (made up of ω-, Asx- and ST-turns), some with characteristic shape, have also been identified. Delineation of composite turns would help in characterizing loops in protein structures, which often have functional roles. Some sequence patterns seen in composites can be used for their incorporation in protein design. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Front propagation in a regular vortex lattice: Dependence on the vortex structure.

PubMed

Beauvier, E; Bodea, S; Pocheau, A

2017-11-01

We investigate the dependence on the vortex structure of the propagation of fronts in stirred flows. For this, we consider a regular set of vortices whose structure is changed by varying both their boundary conditions and their aspect ratios. These configurations are investigated experimentally in autocatalytic solutions stirred by electroconvective flows and numerically from kinematic simulations based on the determination of the dominant Fourier mode of the vortex stream function in each of them. For free lateral boundary conditions, i.e., in an extended vortex lattice, it is found that both the flow structure and the front propagation negligibly depend on vortex aspect ratios. For rigid lateral boundary conditions, i.e., in a vortex chain, vortices involve a slight dependence on their aspect ratios which surprisingly yields a noticeable decrease of the enhancement of front velocity by flow advection. These different behaviors reveal a sensitivity of the mean front velocity on the flow subscales. It emphasizes the intrinsic multiscale nature of front propagation in stirred flows and the need to take into account not only the intensity of vortex flows but also their inner structure to determine front propagation at a large scale. Differences between experiments and simulations suggest the occurrence of secondary flows in vortex chains at large velocity and large aspect ratios.

Long-term secondary prevention of acute myocardial infarction (SEPAT) - guidelines adherence and outcome.

PubMed

Ergatoudes, Constantinos; Thunström, Erik; Rosengren, Annika; Björck, Lena; Bengtsson Boström, Kristina; Falk, Kristin; Fu, Michael

2016-11-17

A number of registry studies have reported suboptimal adherence to guidelines for cardiovascular prevention during the first year after acute myocardial infarction (AMI). However, only a few studies have addressed long-term secondary prevention after AMI. This study evaluates prevention guideline adherence and outcome of guideline-directed secondary prevention in patients surviving 2 years after AMI. Patients aged 18-85 years at the time of their index AMI were consecutively identified from hospital discharge records between July 2010 and December 2011 in Gothenburg, Sweden. All patients who agreed to participate in the study (16.2%) were invited for a structured interview, physical examinations and laboratory analysis 2 years after AMI. Guideline-directed secondary preventive goals were defined as optimally controlled blood pressure, serum cholesterol, glucose, regular physical activity, smoking cessation and pharmacological treatment. The mean age of the study cohort (n = 200) at the index AMI was 63.0 ± 9.7 years, 79% were men. Only 3.5% of the cohort achieved all six guideline-directed secondary preventive goals 2 years after infarction. LDL < 1.8 mmol/L was achieved in 18.5% of the cohort, regular exercise in 45.5% and systolic blood pressure <140 mmHg in 57.0%. Anti-platelet therapy was used by 97% of the patients, beta-blockers by 83.0%, angiotensin-converting enzyme inhibitors/angiotensin receptor blockers by 76.5% and statins by 88.5%. During follow-up, non-fatal adverse cardiovascular events (cardiac hospitalization, recurrent acute coronary syndrome, angina pectoris, new percutaneous coronary intervention, new onset of atrial fibrillation, post-infarct heart failure, pacemaker implantation, stroke/transient ischemic attack (TIA), cardiac surgery and cardiac arrest) occurred in 47% of the cohort and readmission due to cardiac causes in 30%. Our data showed the failure of secondary prevention in our daily clinical practice and high rate of non-fatal adverse cardiovascular events 2 years after AMI.

EMERGING TECHNOLOGY BULLETIN: RECLAMATION OF LEAD FROM SUPERFUND WASTE MATERIAL USING SECONDARY LEAD SMELTERS

EPA Science Inventory

This process involves incorporating lead-contaminated Superfund waste with the regular feed to a secondary lead smelter. Since secondary lead smelters already recover lead from recycled automobile batteries, it seems likely that this technology could be used to treat waste from ...

[Possibilities of dialysis therapy in irreversible renal failure in rheumatoid arthritis with secondary amyloidosis].

PubMed

Vachtenheim, J; Tocík, J; Novák, Z; Zeman, P

1990-11-01

The authors discuss their initial experience with the treatment of secondary amyloidosis in rheumatoid arthritis with irreversible renal failure in patients included in a regular dialyzation programme. The hitherto assembled 15-month experience justifies the inclusion of patients with this cause of irreversible renal failure in a dialyzation programme. The reverse is not only wrong from the medical aspect but is inhuman and interferes with the life of families of these patients. Although the procedure during a regular dialyzation programme of these patients with rheumatoid arthritis with secondary amyloidosis is more complicated, more pretentious and more responsible, it is our medical duty to carry this burden together with the patient.

Chromatin accessibility and guide sequence secondary structure affect CRISPR-Cas9 gene editing efficiency.

PubMed

Jensen, Kristopher Torp; Fløe, Lasse; Petersen, Trine Skov; Huang, Jinrong; Xu, Fengping; Bolund, Lars; Luo, Yonglun; Lin, Lin

2017-07-01

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated protein 9 (CRISPR-Cas9) systems have emerged as the method of choice for genome editing, but large variations in on-target efficiencies continue to limit their applicability. Here, we investigate the effect of chromatin accessibility on Cas9-mediated gene editing efficiency for 20 gRNAs targeting 10 genomic loci in HEK293T cells using both SpCas9 and the eSpCas9(1.1) variant. Our study indicates that gene editing is more efficient in euchromatin than in heterochromatin, and we validate this finding in HeLa cells and in human fibroblasts. Furthermore, we investigate the gRNA sequence determinants of CRISPR-Cas9 activity using a surrogate reporter system and find that the efficiency of Cas9-mediated gene editing is dependent on guide sequence secondary structure formation. This knowledge can aid in the further improvement of tools for gRNA design. © 2017 Federation of European Biochemical Societies.

A Secondary Guy: Physically Disabled Teenagers in Secondary Schools.

ERIC Educational Resources Information Center

Doubt, Lorna; McColl, Mary Ann

2003-01-01

A phenomenological study of seven teenagers with physical disabilities attending a regular secondary school focused on social integration and the factors influencing it. Results showed extrinsic and intrinsic factors that facilitate or limit integration. Occupational therapists can ensure that schools are inclusive and that clients are capable of…

State of Alabama Annual Vocational Education Performance Report for Fiscal Year 1994.

ERIC Educational Resources Information Center

Alabama State Dept. of Education, Montgomery. Div. of Vocational Education Services.

During fiscal year 1994, enrollment in secondary-level vocational education (VE) in Alabama totaled 202,402. Secondary school districts provided VE to 17,037 adult students, and postsecondary institutions provided regular occupational/technical training to 80,764 adults and training for business/industry to 19,723 adults. Secondary and/or…

A study of the thermal denaturation of the S-layer protein from Lactobacillus salivarius

NASA Astrophysics Data System (ADS)

Lighezan, Liliana; Georgieva, Ralitsa; Neagu, Adrian

2012-09-01

Surface layer (S-layer) proteins display an intrinsic self-assembly property, forming monomolecular crystalline arrays, identified in outermost structures of the cell envelope in many organisms, such as bacteria and archaea. Isolated S-layer proteins also possess the ability to recrystallize into regular lattices, being used in biotechnological applications, such as controlling the architecture of biomimetic surfaces. To this end, the stability of the S-layer proteins under high-temperature conditions is very important. In this study, the S-layer protein has been isolated from Lactobacillus salivarius 16 strain of human origin, and purified by cation-exchange chromatography. Using circular dichroism (CD) spectroscopy, we have investigated the thermal denaturation of the S-layer protein. The far- and near-UV CD spectra have been collected, and the temperature dependence of the CD signal in these spectral domains has been analyzed. The variable temperature results show that the secondary and tertiary structures of the S-layer protein change irreversibly due to the heating of the sample. After the cooling of the heated protein, the secondary and tertiary structures are partially recovered. The denaturation curves show that the protein unfolding depends on the sample concentration and on the heating rate. The secondary and tertiary structures of the protein suffer changes in the same temperature range. We have also detected an intermediate state in the protein denaturation pathway. Our results on the thermal behavior of the S-layer protein may be important for the use of S-layer proteins in biotechnological applications, as well as for a better understanding of the structure and function of S-layer proteins.

"Who Takes a Second Chance?" Profile of Participants in Alternative Systems for Obtaining a Secondary Diploma

ERIC Educational Resources Information Center

Glorieux, Ignace; Heyman, Ryfka; Jegers, Marc; Taelman, Maaike

2011-01-01

In Belgium, the Exam Board (EB) and the Secondary School for Adults (SSA) are two different ways to attain a secondary diploma after leaving secondary school without a diploma. The SSA is part of the regular educational system and organises courses with an adult approach. The EB is a flexible system in which students prepare themselves to do…

Self-Esteem of Deaf and Hard of Hearing Students in Regular and Special Schools

ERIC Educational Resources Information Center

Lesar, Irena; Smrtnik Vitulic, Helena

2014-01-01

The study focuses on the self-esteem of deaf and hard of hearing (D/HH) students from Slovenia. A total of 80 D/HH students from regular and special primary schools (grades 6-9) and from regular and special secondary schools (grades 1-4) completed the Self-Esteem Questionnaire (Lamovec 1994). For the entire group of D/HH students, the results of…

Scientific explanations in Greek upper secondary physics textbooks

NASA Astrophysics Data System (ADS)

Velentzas, Athanasios; Halkia, Krystallia

2018-01-01

In this study, an analysis of the structure of scientific explanations included in physics textbooks of upper secondary schools in Greece was completed. In scientific explanations for specific phenomena found in the sample textbooks, the explanandum is a logical consequence of the explanans, which in all cases include at least one scientific law (and/or principle, model or rule) previously presented, as well as statements concerning a specific case or specific conditions. The same structure is also followed in most of the cases in which the textbook authors explain regularities (i.e. laws, rules) as consequences of one or more general law or principle of physics. Finally, a number of the physics laws and principles presented in textbooks are not deduced as consequences from other, more general laws, but they are formulated axiomatically or inductively derived and the authors argue for their validity. Since, as it was found, the scientific explanations presented in the textbooks used in the study have similar structures to the explanations in internationally known textbooks, the findings of the present work may be of interest not only to science educators in Greece, but also to the community of science educators in other countries.

Making It Work: Practical Ideas for Integrating Exceptional Children into Regular Classes.

ERIC Educational Resources Information Center

Aiello, Barbara, Ed.

Intended for special education and regular teachers, the guide contains brief articles on the nature of mainstreaming handicapped children; mainstreaming models at the preschool, elementary school, and secondary school levels; specific suggestions for setting up mainstreaming programs, and interviews with five persons involved in mainstream…

[Family Health Program implementation in municipalities in Mato Grosso State, Brazil].

PubMed

Canesqui, Ana Maria; Spinelli, Maria Angélica do Santos

2008-04-01

This article analysis some key aspects in the implementation of the Family Health Program (FHP): results; conditions; and institutional mechanisms; flow and regularity of funding; organizational structures; and human resources availability and training. The study was conducted in seven municipalities (counties) in the State of Mato Grosso, Brazil, and used secondary data as well as primary data from interviews with different stakeholders. The research design was evaluative, using a quantitative/qualitative analysis. The results showed: varying stages in the implementation process, different FHP models, and adaptation of organizational structures; high level of human resources availability, except for nurse assistants; availability of financial resources, with some difficulties in their flow; and other institutional factors that hinder or facilitate the micro-implementation process in the municipalities.

"Clear Educational Routes": An Example of Conservative Modernization in Swedish Upper Secondary Schools

ERIC Educational Resources Information Center

Loeb, Ingrid Henning; Wass, Karin Lumsden

2015-01-01

This article concerns the development of education for young students in Sweden who do not attend regular pathways in upper secondary education, and analyses the changes of educational policy and the organizing of teaching for this group of students. The centre of interest is the upper secondary educational reform carried out in 2011. With this…

Evaluation of Bilingual Secondary Education in the Netherlands: Students' Language Proficiency in English

ERIC Educational Resources Information Center

Admiraal, Wilfried; Westhoff, Gerard; de Bot, Kees

2006-01-01

In this longitudinal study, we examined the effects of the use of English as the language of instruction in the first 4 years of secondary education in The Netherlands on the students' language proficiency in English and Dutch, and achievement in subject matters taught through English. Compared to a control group in regular secondary education,…

Comparative morphology of the axial complex and interdependence of internal organ systems in sea urchins (Echinodermata: Echinoidea).

PubMed

Ziegler, Alexander; Faber, Cornelius; Bartolomaeus, Thomas

2009-06-09

The axial complex of echinoderms (Echinodermata) is composed of various primary and secondary body cavities that interact with each other. In sea urchins (Echinoidea), structural differences of the axial complex in "regular" and irregular species have been observed, but the reasons underlying these differences are not fully understood. In addition, a better knowledge of axial complex diversity could not only be useful for phylogenetic inferences, but improve also an understanding of the function of this enigmatic structure. We therefore analyzed numerous species of almost all sea urchin orders by magnetic resonance imaging, dissection, histology, and transmission electron microscopy and compared the results with findings from published studies spanning almost two centuries. These combined analyses demonstrate that the axial complex is present in all sea urchin orders and has remained structurally conserved for a long time, at least in the "regular" species. Within the Irregularia, a considerable morphological variation of the axial complex can be observed with gradual changes in topography, size, and internal architecture. These modifications are related to the growing size of the gastric caecum as well as to the rearrangement of the morphology of the digestive tract as a whole. The structurally most divergent axial complex can be observed in the highly derived Atelostomata in which the reorganization of the digestive tract is most pronounced. Our findings demonstrate a structural interdependence of various internal organs, including digestive tract, mesenteries, and the axial complex.

The Regular Education Initiative in the Anchorage Public Schools.

ERIC Educational Resources Information Center

Kennedy, Sylvia

The study examined the number of Anchorage (Alaska) public schools that are using the Regular Education Initiative (REI) concept in their special education programs and the attitudes of building principals concerning both REI and collaborative consultation. Surveys mailed to 65 principals yielded a return of 30 questionnaires (6 secondary and 24…

Are General Educators Prepared To Teach Students with Physical Disabilities?

ERIC Educational Resources Information Center

Singh, Delar K.

This paper discusses the outcomes of a study that investigated the knowledge base and professional readiness of 50 regular education teachers for the inclusion of learners who have physical disabilities. Members of the sample were regular elementary and secondary teachers who were enrolled in a graduate teacher education program at a private…

Earth: Physico-mathematical Meaning of "primary" and "secondary" Oceans Conception

NASA Astrophysics Data System (ADS)

Kochemasov, G.

Geologists term the Pacific ocean "primary" and Atlantic and Indian oceans "sec- ondary" meaning that the first is larger, deeper, older (?) and plays more fundamental role in the Earth's tectonics. The wave planetology as hierarchically higher than geol- ogy (Earth is only one of planets and of many celestial bodies), states that all celestial bodies are dichotomic ( "Pacific" as a tectonic feature is found in any celestial body) and sectoral (i.g., the Arctic-Antarctic symptom is also in any body) (Theorems 1, 2 [1]). The tectonic dichotomy and sectoring are related to the first and second harmon- ica (wave1 and wave2) of warping standing waves appearing in any body just because they move in non-circular (elliptic, parabolic) orbits and hence inertia forces tend to distort original shapes. This disfiguring of a rotating body is not just a superficial fea- ture, it involves fundamental changes in the entire vertical section above and below surface rises and falls (Theorem 4 [1]). Here acts the law of angular momentum equi- libration. Thus, under the Pacific basin hollow -the deepest hollow produced by wave1 - mantle is denser than under the Atlantic and Indian oceanic basins - basins produced by wave2. We know it because squeezed out of mantle tholeiites in the mid-oceanic ridges are Fe-richer in Pacific than in other oceans. The "primary" ocean is thus a fundamental or "wave1" or 2pR-structure. The "secondary" oceans are "wave2" or pR-structures. pR-structures represented by continents, secondary oceans and basins and the "superswell" (Darwin rise) in the Pacific, i.e. by most important terrestrial lithospheric tectonic blocks, are distributed on the Earth's surface not randomly. As must be expected of the standing wave interference picture, the pR-structure pattern shows regular grouping around certain centres. There are 6 centres - vertices of an oc- tahedron occurring at equator (1, 2), tropics (3, 4) and polar circles (5, 6). They are: 1. New Guinea, 2. Equatorial Atlantic, 3. Easter Isl., 4. the Pamirs-Hindukush, 5. Bering Strait, 6. Bouvet Isl. There is expected antipodality between 1-2, 3-4, 5-6. The vertices of the structural octahedron combine around them sectors by a similar algorithm: there always converge two opposite differently uplifted sectors separated by two differently 1 subsided sectors. I.g., around the Pamirs-Hindukush there are two uplifted sectors: African (++) Asian (+), and two separating them subsided ones: Eurasian (-) Indo- ceanic (- -). The cosmically oriented structural octahedron and other regularities show that the wave induced structurization is a real predominant factor in planetology. Ref. [1] Kochemasov G.G.(1999) Geophys.Res.Abstr., v.1, 3, 700. 2

The Influence of Class Management and Student Guidance upon Academic Work at the Elementary and Lower Secondary Education Levels in Japan.

ERIC Educational Resources Information Center

Kataoka, Tokuo

An important aspect of Japanese schooling is the attention given to class management and student guidance, particularly at the elementary and lower secondary levels. The Japanese school curriculum for the elementary and the lower secondary schools consists of three areas: (1) regular subjects; (2) moral education; and (3) special activities. The…

34 CFR 206.5 - What definitions apply to these programs?

Code of Federal Regulations, 2013 CFR

2013-07-01

... ENGAGED IN MIGRANT AND OTHER SEASONAL FARMWORK-HIGH SCHOOL EQUIVALENCY PROGRAM AND COLLEGE ASSISTANCE... Elementary school EDGAR Facilities Minor remodeling Nonprofit Private Project Public Secondary school... secondary school; (iii) Is a public or nonprofit institution; (iv) Admits as a regular student only a person...

34 CFR 206.5 - What definitions apply to these programs?

Code of Federal Regulations, 2011 CFR

2011-07-01

... ENGAGED IN MIGRANT AND OTHER SEASONAL FARMWORK-HIGH SCHOOL EQUIVALENCY PROGRAM AND COLLEGE ASSISTANCE... Elementary school EDGAR Facilities Minor remodeling Nonprofit Private Project Public Secondary school... secondary school; (iii) Is a public or nonprofit institution; (iv) Admits as a regular student only a person...

34 CFR 206.5 - What definitions apply to these programs?

Code of Federal Regulations, 2012 CFR

2012-07-01

... ENGAGED IN MIGRANT AND OTHER SEASONAL FARMWORK-HIGH SCHOOL EQUIVALENCY PROGRAM AND COLLEGE ASSISTANCE... Elementary school EDGAR Facilities Minor remodeling Nonprofit Private Project Public Secondary school... secondary school; (iii) Is a public or nonprofit institution; (iv) Admits as a regular student only a person...

34 CFR 206.5 - What definitions apply to these programs?

Code of Federal Regulations, 2014 CFR

2014-07-01

... ENGAGED IN MIGRANT AND OTHER SEASONAL FARMWORK-HIGH SCHOOL EQUIVALENCY PROGRAM AND COLLEGE ASSISTANCE... Elementary school EDGAR Facilities Minor remodeling Nonprofit Private Project Public Secondary school... secondary school; (iii) Is a public or nonprofit institution; (iv) Admits as a regular student only a person...

Poly-amido-saccharides: Synthesis via Anionic Polymerization of a β-Lactam Sugar Monomer

PubMed Central

Dane, Eric L.; Grinstaff, Mark W.

2013-01-01

Chiral poly-amido-saccharides (PASs) with a defined molecular weight and narrow polydispersity are synthesized using an anionic ring-opening polymerization of a β-lactam sugar monomer. The PASs have a previously unreported main chain structure that is composed of pyranose rings linked through the 1- and 2-positions by an amide bond with α-stereochemistry. The monomer is synthesized in one-step from benzyl-protected d-glucal and polymerized using mild reaction conditions to give degrees of polymerization ranging from 25 to >150 in high yield. Computational modeling reveals how the monomer’s structure and steric bulk affect the thermodynamics and kinetics of polymerization. Protected and deprotected polymers and model compounds are characterized using a variety of methods (NMR, GPC, IR, DLS, etc.). Reductive debenzylation provides the deprotected, hydrophilic polymers in high yield. Based on circular dichroism, the deprotected polymers possess a regular secondary structure in aqueous solution, which agrees favorably with the prediction of a helical structure using molecular modeling. Furthermore, we provide evidence suggesting that the polymers bind the lectin concanavalin A at the same site as natural carbohydrates, showing the potential of these polymers to mimic natural polysaccharides. PASs offer the advantages associated with synthetic polymers, such as greater control over structure and derivitization, and less batch-to-batch variation. At the same time, they preserve many of the structural features of natural polysaccharides, such as a stereochemically regular, rigid pyranose backbone, that make natural carbohydrate polymers important materials both for their unique properties and useful applications. PMID:22937875

Curriculum and Methods (EDS 300).

ERIC Educational Resources Information Center

McNaughton, Robert H.; And Others

This course is a team taught, 12 quarter-hour block course, which combines a general teaching, competency segment and a specialized subject area methods segment. It is required of all students seeking secondary certification and is supported out of the regular secondary department budget. The teaching competency segment has the following three…

An Analysis of Teacher Sorting in Secondary Special Education and Alternative Schools

ERIC Educational Resources Information Center

Mason-Williams, Loretta; Gagnon, Joseph Calvin

2017-01-01

This study provides nationally representative information about the qualifications and preparation of secondary content and special education teachers in special education and alternative school settings, as compared with teachers in regular schools. Findings demonstrate that a statistically significant relationship did not exist between school…

The Learning Enrichment Service: A Triad-Based Secondary School Model for Enrichment Programming.

ERIC Educational Resources Information Center

Smyth, Elizabeth; And Others

1983-01-01

Three secondary teachers describe a school-wide support system for meeting the needs of gifted students in and beyond the regular classroom. A management team coordinates enrichment within the school and community while a computerized data bank of enrichment resources is accessible to all learners. (CL)

Title VII Evaluation, 1987-88.

ERIC Educational Resources Information Center

Baenen, Nancy R.; Yonan, Barbara

Title VII federal funds have been used in the Austin (Texas) Independent School District (AISD) since 1985-86 to enhance the regular secondary bilingual and English-as-a-second-language programs for Hispanic limited English proficient (LEP) students. The four secondary campuses involved were those with the highest concentrations of Hispanic LEP…

Increasing Organizational Skills and Homework Productivity with Ninth Grade Emotionally Handicapped and Regular Students.

ERIC Educational Resources Information Center

Birnbaum, Barry W.

The practicum was designed to increase the organizational skills of four emotionally handicapped students (aged 13-14) enrolled in a secondary school program, and to increase the quantity and quality of homework completed by those students in a regular English class. A needs survey documented that students, parents, and teachers felt that…

Inclusive Education in Spain: How Do Skills, Resources, and Supports Affect Regular Education Teachers' Perceptions of Inclusion?

ERIC Educational Resources Information Center

Chiner, Esther; Cardona, Maria Cristina

2013-01-01

This study examined regular education teachers' perceptions of inclusion in elementary and secondary schools in Spain and how these perceptions may differ depending on teaching experience, skills, and the availability of resources and supports. Stratified random sampling procedures were used to draw a representative sample of 336 general education…

Regular Classroom Teachers' Attitudes toward Mainstreaming the Emotionally Disturbed: Can They Be Changed?

ERIC Educational Resources Information Center

Beare, Paul L.

This study reviews the effects of training and service in a student advocacy program for Emotionally Disturbed (ED) children on attitudes of 16 secondary teachers toward ED children in the regular class. The intervention program involved 6 days of inservice training on working with ED students, delivered concurrent with the teachers' serving in an…

The Integration of Children with Disabilities into Regular Schools. A Naturalistic Study. Stage 2 Report.

ERIC Educational Resources Information Center

Center, Yola; And Others

The study used a multiple case study method to investigate the quality of the educational and social experiences of elementary-level and secondary-level children with disabilities currently integrated within the Australian regular school system. This second stage of the study used for its sample 23 children with intellectual disabilities, 18 with…

Recognition Memory for Novel Stimuli: The Structural Regularity Hypothesis

ERIC Educational Resources Information Center

Cleary, Anne M.; Morris, Alison L.; Langley, Moses M.

2007-01-01

Early studies of human memory suggest that adherence to a known structural regularity (e.g., orthographic regularity) benefits memory for an otherwise novel stimulus (e.g., G. A. Miller, 1958). However, a more recent study suggests that structural regularity can lead to an increase in false-positive responses on recognition memory tests (B. W. A.…

Comprehensive computational design of ordered peptide macrocycles

PubMed Central

Hosseinzadeh, Parisa; Bhardwaj, Gaurav; Mulligan, Vikram Khipple; Shortridge, Matthew D.; Craven, Timothy W.; Pardo-Avila, Fátima; Rettie, Stephen A.; Kim, David E.; Silva, Daniel-Adriano; Ibrahim, Yehia M.; Webb, Ian K.; Cort, John R.; Adkins, Joshua N.; Varani, Gabriele; Baker, David

2018-01-01

Mixed-chirality peptide macrocycles such as cyclosporine are among the most potent therapeutics identified to date, but there is currently no way to systematically search the structural space spanned by such compounds. Natural proteins do not provide a useful guide: Peptide macrocycles lack regular secondary structures and hydrophobic cores, and can contain local structures not accessible with L-amino acids. Here, we enumerate the stable structures that can be adopted by macrocyclic peptides composed of L- and D-amino acids by near-exhaustive backbone sampling followed by sequence design and energy landscape calculations. We identify more than 200 designs predicted to fold into single stable structures, many times more than the number of currently available unbound peptide macrocycle structures. Nuclear magnetic resonance structures of 9 of 12 designed 7- to 10-residue macrocycles, and three 11- to 14-residue bicyclic designs, are close to the computational models. Our results provide a nearly complete coverage of the rich space of structures possible for short peptide macrocycles and vastly increase the available starting scaffolds for both rational drug design and library selection methods. PMID:29242347

An unusual xylan in Arabidopsis primary cell walls is synthesised by GUX3, IRX9L, IRX10L and IRX14

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

Mortimer, Jenny C.; Faria-Blanc, Nuno; Yu, Xiaolan

Xylan is a crucial component of many plant primary and secondary cell walls. However, the structure and function of xylan in the dicotyledon primary cell wall is not well understood. Here, we characterized a xylan that is specific to tissues enriched in Arabidopsis primary cell walls. Unlike previously described xylans, this xylan carries a pentose linked 1–2 to the α-1,2-d-glucuronic acid (GlcA) side chains on the β-1,4-Xyl backbone. The frequent and precisely regular spacing of GlcA substitutions every six xylosyl residues along the backbone is also unlike that previously observed in secondary cell wall xylan. Molecular genetics, in vitro assays,more » and expression data suggest that IRX9L, IRX10L and IRX14 are required for xylan backbone synthesis in primary cell wall synthesising tissues. IRX9 and IRX10 are not involved in the primary cell wall xylan synthesis but are functionally exchangeable with IRX9L and IRX10L. GUX3 is the only glucuronyltransferase required for the addition of the GlcA decorations on the xylan. Lastly, the differences in xylan structure in primary versus secondary cell walls might reflect the different roles in cross-linking and interaction with other cell wall components.« less

An unusual xylan in Arabidopsis primary cell walls is synthesised by GUX3, IRX9L, IRX10L and IRX14

DOE PAGES

Mortimer, Jenny C.; Faria-Blanc, Nuno; Yu, Xiaolan; ...

2015-06-04

Xylan is a crucial component of many plant primary and secondary cell walls. However, the structure and function of xylan in the dicotyledon primary cell wall is not well understood. Here, we characterized a xylan that is specific to tissues enriched in Arabidopsis primary cell walls. Unlike previously described xylans, this xylan carries a pentose linked 1–2 to the α-1,2-d-glucuronic acid (GlcA) side chains on the β-1,4-Xyl backbone. The frequent and precisely regular spacing of GlcA substitutions every six xylosyl residues along the backbone is also unlike that previously observed in secondary cell wall xylan. Molecular genetics, in vitro assays,more » and expression data suggest that IRX9L, IRX10L and IRX14 are required for xylan backbone synthesis in primary cell wall synthesising tissues. IRX9 and IRX10 are not involved in the primary cell wall xylan synthesis but are functionally exchangeable with IRX9L and IRX10L. GUX3 is the only glucuronyltransferase required for the addition of the GlcA decorations on the xylan. Lastly, the differences in xylan structure in primary versus secondary cell walls might reflect the different roles in cross-linking and interaction with other cell wall components.« less

Optically active polyurethane@indium tin oxide nanocomposite: Preparation, characterization and study of infrared emissivity

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

Yang, Yong; Zhou, Yuming, E-mail: ymzhou@seu.edu.cn; Ge, Jianhua

Highlights: ► Silane coupling agent of KH550 was used to connect the ITO and polyurethanes. ► Infrared emissivity values of the hybrids were compared and analyzed. ► Interfacial synergistic action and orderly secondary structure were the key factors. -- Abstract: Optically active polyurethane@indium tin oxide and racemic polyurethane@indium tin oxide nanocomposites (LPU@ITO and RPU@ITO) were prepared by grafting the organics onto the surfaces of modified ITO nanoparticles. LPU@ITO and RPU@ITO composites based on the chiral and racemic tyrosine were characterized by FT-IR, UV–vis spectroscopy, X-ray diffraction (XRD), SEM, TEM, and thermogravimetric analysis (TGA), and the infrared emissivity values (8–14 μm)more » were investigated in addition. The results indicated that the polyurethanes had been successfully grafted onto the surfaces of ITO without destroying the crystalline structure. Both composites possessed the lower infrared emissivity values than the bare ITO nanoparticles, which indicated that the interfacial interaction had great effect on the infrared emissivity. Furthermore, LPU@ITO based on the optically active polyurethane had the virtue of regular secondary structure and more interfacial synergistic actions between organics and inorganics, thus it exhibited lower infrared emissivity value than RPU@ITO based on the racemic polyurethane.« less

Exploiting Photo-induced Reactions in Polymer Blends to Create Hierarchically Ordered, Defect-free Materials

ScienceCinema

Balazs, Anna [University of Pittsburgh, Pittsburgh, Pennsylvania, United States

2017-12-09

Computer simulations reveal how photo-induced chemical reactions can be exploited to create long-range order in binary and ternary polymeric materials. The process is initiated by shining a spatially uniform light over a photosensitive AB binary blend, which undergoes both a reversible chemical reaction and phase separation. We then introduce a well-collimated, higher-intensity light source. Rastering this secondary light over the sample locally increases the reaction rate and causes formation of defect-free, spatially periodic structures. These binary structures resemble either the lamellar or hexagonal phases of microphase-separated di-block copolymers. We measure the regularity of the ordered structures as a function of the relative reaction rates for different values of the rastering speed and determine the optimal conditions for creating defect-free structures in the binary systems. We then add a non-reactive homo-polymer C, which is immiscible with both A and B. We show that this component migrates to regions that are illuminated by the secondary, higher-intensity light, allowing us to effectively write a pattern of C onto the AB film. Rastering over the ternary blend with this collimated light now leads to hierarchically ordered patterns of A, B, and C. The findings point to a facile, non-intrusive process for manufacturing high-quality polymeric devices in a low-cost, efficient manner.

[Tobacco use by adolescents in Barcelona (Spain) and trends in the last 20 years].

PubMed

Ariza, Carles; García-Continente, Xavier; Villalbí, Joan Ramon; Sánchez-Martínez, Francesca; Pérez, Anna; Nebot, Manel

2014-01-01

Smoking is a preventable cause of early death and the habit starts in adolescence. The aim of this study was to describe tobacco consumption in secondary school students in 2008 and trends in the last 20 years in Barcelona. We analyzed the trend in tobacco consumption by comparing data from 8 surveys carried out between 1987 and 2008 in the 8th (2nd year of Compulsory Secondary Education), 10th (4th year of Compulsory Secondary Education) and 12th (2nd year of Compulsory Secondary Education) years of secondary school. The FRESC questionnaire was used. Data on regular and daily consumption and associated factors in 2008 were gathered and compared with those corresponding to the previous studies. Percentages of annual change were calculated with Joinpoint regression and data were stratified by sex and year of education. In 2008, 6.1% of boys and 4.5% of girls in the 8th year, 15.8% and 20.4% of those in the 10th year, respectively, and 26.1% and 33.1% of those in the 12th year, respectively, were regular smokers. A strong association was noted between regular smoking and cannabis consumption in three school years, as well as with having friends who were smokers and poor school performance. At 15-16 years old, the average annual decrease from 1996 to 2008 was 6.8% in girls and 6.1% in boys. Adolescent smoking has been decreasing in the last few years in Barcelona. There is a strong association between tobacco use and cannabis consumption. Copyright © 2013 SESPAS. Published by Elsevier Espana. All rights reserved.

Interventions Employed in Regular Education Settings for Secondary Students with High Functioning Autism: A Meta-Analysis

ERIC Educational Resources Information Center

McKeithan, Glennda Kashner

2016-01-01

An increase has occurred in the number of students identified as having high functioning autism (HFA), who are being served in the regular education setting with their non-disabled peers. Many of these students have difficulty with academic and social expectations in this setting, and a minimal amount of information is available to educators…

Social dimensions of inclusion in education of 4th and 7th grade pupils in inclusive and regular classes: Outcomes from Austria.

PubMed

Schwab, Susanne

2015-01-01

Positive peer relationships play a significant role in the development of students. They are beneficial for learning and psychological outcomes. This article draws upon an important distinction between the four main themes of social participation (friendships, interactions, peer acceptance and self-perception of social participation) and examines these aspects in inclusive and regular classes. Especially, differences in social participation of students with and without special educational needs (SEN) in inclusive classes and between students without SEN in inclusive and regular classes are examined. In this study, data from 1115 pupils in primary and secondary schools in Austria were analysed, of which 129 were diagnosed as having SEN. The results showed that in inclusive classes, students with SEN had lower scores on all four subthemes of social participation (friendships, interactions, peer acceptance and self-perception of social integration) than students without SEN. Regarding students without SEN, friendships and peer acceptance were significantly higher in inclusive classes than in regular classes. Differences were neither found for gender, nor between primary and secondary school students. Copyright © 2015 Elsevier Ltd. All rights reserved.

Detection of Ludic Patterns in Two Triadic Motor Games and Differences in Decision Complexity

PubMed Central

Aguilar, Miguel Pic; Navarro-Adelantado, Vicente; Jonsson, Gudberg K.

2018-01-01

The triad is a particular structure in which an ambivalent social relationship takes place. This work is focused on the search of behavioral regularities in the practice of motor games in triad, which is a little known field. For the detection of behavioral patterns not visible to the naked eye, we use Theme. A chasing games model was followed, with rules, and in two different structures (A↔B↔C↔A and A → B → C → A) on four class groups (two for each structure), for a total of 84, 12, and 13 year old secondary school students, 37 girls (44%) and 47 boys (56%). The aim was to examine if the players' behavior, in relation to the triad structure, matches with any ludic behavior patterns. An observational methodology was applied, with a nomothetic, punctual and multidimensional design. The intra and inter-evaluative correlation coefficients and the generalizability theory ensured the quality of the data. A mixed behavioral role system was used (four criteria and 15 categories), and the pattern detection software Theme was applied to detect temporal regularities in the order of event occurrences. The results show that time location of motor responses in triad games was not random. In the “maze” game we detected more complex ludic patterns than the “three fields” game, which might be explained by means of structural determinants such as circulation. This research points out the decisional complexity in motor games, and it confirms the differences among triads from the point of view of motor communication. PMID:29354084

Navigating the Challenges of Delivering Secondary School Courses by Videoconference

ERIC Educational Resources Information Center

Rehn, Nicole; Maor, Dorit; McConney, Andrew

2017-01-01

The purpose of this research is to unpack and learn from the experiences of teachers who deliver courses to remote secondary school students by videoconference. School districts are using videoconferencing to connect students and teachers who are separated geographically through regular live, real-time conferences. Previous studies have shown the…

Instructors' Use of Technology in Post-Secondary Undergraduate Mathematics Teaching: A Local Study

ERIC Educational Resources Information Center

Jesso, A. T.; Kondratieva, M. F.

2016-01-01

In this study, instructors of undergraduate mathematics from post-secondary institutions in Newfoundland were surveyed (N = 13) and interviewed (N = 8) about their use of, experiences with, and views on, technologically assisted teaching. It was found that the majority of them regularly use technologies for organizational and communication…

The development of structures in analogue and natural debris avalanches

NASA Astrophysics Data System (ADS)

Paguican, Engielle Mae; van Wyk de Vries, Benjamin; Mahar Francisco Lagmay, Alfredo; Grosse, Pablo

2010-05-01

All types of rockslide-debris avalanches present a plethora of internal structures that are also well observed on the surface. Many of these are seen as faults and folds that can be used to determine deformation history and kinematics. We present two sets of simple and well-constrained experiments of reduced basal friction laboratory rockslides, equivalent to a highly deformed simple shear layer, with plug-flow. These follow the original ramp-slide work of Shea and van Wyk de Vries (Geosphere, 2008). The experiments used a curved ramp where materials accelerate until reaching a gently-sloped depositional surface and a constantly inclined ramp with a more regular slope and longer slides. A detailed description of deposit structures, their sequential formation and morphology is then used to investigate the transport type and deformation chronology from slide initiation to runout stopping of avalanches. Results using a curved ramp show accumulation and thickening at where the slope decreases. The thickened mass then further remobilises and advances by secondary collapse of the mass. Such a stop-start process may be important in many mountainous avalanches where there are rapid changes in slope. The constantly inclined ramp shows shearing and extensional structures at the levees and a set of compression and extension structures in the middle. We noted that frontal accumulation during flow occurs as materials at the front move slower relative to those in the medial and proximal zones. This also leads to secondary frontal collapse, and helps to maintain a thicker mass that can flow further. Descriptions and analyses of these structures are then applied to the kinematics and dynamics of natural examples. We study the 2006 Guinsaugon Rockslide event in the Philippines and find that frontal accumulation and secondary avalanching had also occurred and were important in determining the distribution and runout of the mass. Frontal bulking and collapse may also have occurred at the Tacna Avalanche, Peru and the Pajonales-Aracar event in Argentina.

DichroCalc: Improvements in Computing Protein Circular Dichroism Spectroscopy in the Near-Ultraviolet.

PubMed

Jasim, Sarah B; Li, Zhuo; Guest, Ellen E; Hirst, Jonathan D

2017-12-16

A fully quantitative theory connecting protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. The web server DichroCalc (http://comp.chem.nottingham.ac.uk/dichrocalc) allows one to compute from first principles the electronic circular dichroism spectrum of a (modeled or experimental) protein structure or ensemble of structures. The regular, repeating, chiral nature of secondary structure elements leads to intense bands in the far-ultraviolet (UV). The near-UV bands are much weaker and have been challenging to compute theoretically. We report some advances in the accuracy of calculations in the near-UV, realized through the consideration of the vibrational structure of the electronic transitions of aromatic side chains. The improvements have been assessed over a set of diverse proteins. We illustrate them using bovine pancreatic trypsin inhibitor and present a new, detailed analysis of the interactions which are most important in determining the near-UV circular dichroism spectrum. Copyright © 2018. Published by Elsevier Ltd.

URS DataBase: universe of RNA structures and their motifs.

PubMed

Baulin, Eugene; Yacovlev, Victor; Khachko, Denis; Spirin, Sergei; Roytberg, Mikhail

2016-01-01

The Universe of RNA Structures DataBase (URSDB) stores information obtained from all RNA-containing PDB entries (2935 entries in October 2015). The content of the database is updated regularly. The database consists of 51 tables containing indexed data on various elements of the RNA structures. The database provides a web interface allowing user to select a subset of structures with desired features and to obtain various statistical data for a selected subset of structures or for all structures. In particular, one can easily obtain statistics on geometric parameters of base pairs, on structural motifs (stems, loops, etc.) or on different types of pseudoknots. The user can also view and get information on an individual structure or its selected parts, e.g. RNA-protein hydrogen bonds. URSDB employs a new original definition of loops in RNA structures. That definition fits both pseudoknot-free and pseudoknotted secondary structures and coincides with the classical definition in case of pseudoknot-free structures. To our knowledge, URSDB is the first database supporting searches based on topological classification of pseudoknots and on extended loop classification.Database URL: http://server3.lpm.org.ru/urs/. © The Author(s) 2016. Published by Oxford University Press.

URS DataBase: universe of RNA structures and their motifs

PubMed Central

Baulin, Eugene; Yacovlev, Victor; Khachko, Denis; Spirin, Sergei; Roytberg, Mikhail

2016-01-01

The Universe of RNA Structures DataBase (URSDB) stores information obtained from all RNA-containing PDB entries (2935 entries in October 2015). The content of the database is updated regularly. The database consists of 51 tables containing indexed data on various elements of the RNA structures. The database provides a web interface allowing user to select a subset of structures with desired features and to obtain various statistical data for a selected subset of structures or for all structures. In particular, one can easily obtain statistics on geometric parameters of base pairs, on structural motifs (stems, loops, etc.) or on different types of pseudoknots. The user can also view and get information on an individual structure or its selected parts, e.g. RNA–protein hydrogen bonds. URSDB employs a new original definition of loops in RNA structures. That definition fits both pseudoknot-free and pseudoknotted secondary structures and coincides with the classical definition in case of pseudoknot-free structures. To our knowledge, URSDB is the first database supporting searches based on topological classification of pseudoknots and on extended loop classification. Database URL: http://server3.lpm.org.ru/urs/ PMID:27242032

5 CFR 532.203 - Structure of regular wage schedules.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Structure of regular wage schedules. 532.203 Section 532.203 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PREVAILING RATE SYSTEMS Prevailing Rate Determinations § 532.203 Structure of regular wage schedules. (a...

Inclusive Education for Students with Hearing Impairment in the Regular Secondary Schools in the North-West Region of Cameroon: Initiatives and Challenges

ERIC Educational Resources Information Center

Bamu, Beryl Ndongwa; De Schauwer, Elisabeth; Verstraete, Sara; Van Hove, Geert

2017-01-01

Although some initiatives are implemented in the education of students with hearing impairments in the regular school, challenges are still encountered in their education. This article which is part of the results from an ongoing qualitative study in the North-West region of Cameroon addresses the different initiatives and challenges involved with…

Marketized Private Tutoring as a Supplement to Regular Schooling: Liberal Studies and the Shadow Sector in Hong Kong Secondary Education

ERIC Educational Resources Information Center

Chan, Claudia; Bray, Mark

2014-01-01

Around the world, increasing numbers of students receive after-school private supplementary tutoring. Such tutoring may be provided through informal channels or by companies, and it may be received one-to-one, in small groups or in large classes. The tutoring is commonly called shadow education since its content mimics that of regular schooling.…

Pi-Pi contacts are an overlooked protein feature relevant to phase separation

PubMed Central

Vernon, Robert McCoy; Chong, Paul Andrew; Tsang, Brian; Kim, Tae Hun; Bah, Alaji; Farber, Patrick; Lin, Hong

2018-01-01

Protein phase separation is implicated in formation of membraneless organelles, signaling puncta and the nuclear pore. Multivalent interactions of modular binding domains and their target motifs can drive phase separation. However, forces promoting the more common phase separation of intrinsically disordered regions are less understood, with suggested roles for multivalent cation-pi, pi-pi, and charge interactions and the hydrophobic effect. Known phase-separating proteins are enriched in pi-orbital containing residues and thus we analyzed pi-interactions in folded proteins. We found that pi-pi interactions involving non-aromatic groups are widespread, underestimated by force-fields used in structure calculations and correlated with solvation and lack of regular secondary structure, properties associated with disordered regions. We present a phase separation predictive algorithm based on pi interaction frequency, highlighting proteins involved in biomaterials and RNA processing. PMID:29424691

Attitudes of Secondary School Teachers towards Inclusive Education in New Delhi, India

ERIC Educational Resources Information Center

Bhatnagar, Nisha; Das, Ajay

2014-01-01

This study was undertaken to determine the attitudes of secondary regular schoolteachers towards the inclusion of students with disabilities in New Delhi. A total of 470 teachers, working in schools managed by a private organisation in Delhi, returned the completed survey. A two-part questionnaire was used in this study. Part one gathered…

Development of a Mobile-Optimised Website to Support Students with Special Needs Transitioning from Primary to Secondary Settings

ERIC Educational Resources Information Center

Chambers, Dianne; Coffey, Anne

2013-01-01

With an increasing number of students with special needs being included in regular classroom environments, consideration of, and planning for, a smooth transition between different school settings is important for parents, classroom teachers and school administrators. The transition between primary and secondary school can be difficult for…

Body weight, exercise and menstrual status among ballet dancers in training.

PubMed

Abraham, S F; Beumont, P J; Fraser, I S; Llewellyn-Jones, D

1982-07-01

A prospective study of the menstrual pattern and weight changes was made in the first year of training of 29 new female entrants to a professional ballet school. Seventy-nine per cent of the student girls had menstrual disturbances at entry: primary amenorrhoea, four; secondary amenorrhoea, 11; irregular menses, eight. The incidence of secondary amenorrhoea increase substantially by the end of the year (20), but was not associated with any significant change in body weight. Only three students menstruated regularly during the year. Menstrual regularity improved during periods of injury and long vacation and it appears that deterioration of the menstrual pattern during dancing periods was related to strenuous physical exercise rather than to any change in body weight.

Evaluating the dose to the contralateral breast when using a dynamic wedge versus a regular wedge.

PubMed

Weides, C D; Mok, E C; Chang, W C; Findley, D O; Shostak, C A

1995-01-01

The incidence of secondary cancers in the contralateral breast after primary breast irradiation is several times higher than the incidence of first time breast cancer. Studies have shown that the scatter radiation to the contralateral breast may play a large part in the induction of secondary breast cancers. Factors that may contribute to the contralateral breast dose may include the use of blocks, the orientation of the field, and wedges. Reports have shown that the use of regular wedges, particularly for the medial tangential field, gives a significantly higher dose to the contralateral breast compared to an open field. This paper compares the peripheral dose outside the field using a regular wedge, a dynamic wedge, and an open field technique. The data collected consisted of measurements taken with patients, solid water and a Rando phantom using a Varian 2300CD linear accelerator. Ion chambers, thermoluminescent dosimeters (TLD), diodes, and films were the primary means for collecting the data. The measurements show that the peripheral dose outside the field using a dynamic wedge is close to that of open fields, and significantly lower than that of regular wedges. This information indicates that when using a medial wedge, a dynamic wedge should be used.

SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data

PubMed Central

Poulsen, Line Dahl; Kielpinski, Lukasz Jan; Salama, Sofie R.; Krogh, Anders; Vinther, Jeppe

2015-01-01

Selective 2′ Hydroxyl Acylation analyzed by Primer Extension (SHAPE) is an accurate method for probing of RNA secondary structure. In existing SHAPE methods, the SHAPE probing signal is normalized to a no-reagent control to correct for the background caused by premature termination of the reverse transcriptase. Here, we introduce a SHAPE Selection (SHAPES) reagent, N-propanone isatoic anhydride (NPIA), which retains the ability of SHAPE reagents to accurately probe RNA structure, but also allows covalent coupling between the SHAPES reagent and a biotin molecule. We demonstrate that SHAPES-based selection of cDNA–RNA hybrids on streptavidin beads effectively removes the large majority of background signal present in SHAPE probing data and that sequencing-based SHAPES data contain the same amount of RNA structure data as regular sequencing-based SHAPE data obtained through normalization to a no-reagent control. Moreover, the selection efficiently enriches for probed RNAs, suggesting that the SHAPES strategy will be useful for applications with high-background and low-probing signal such as in vivo RNA structure probing. PMID:25805860

Profiling interest of students in science: Learning in school and beyond

NASA Astrophysics Data System (ADS)

Dierks, Pay O.; Höffler, Tim N.; Parchmann, Ilka

2014-05-01

Background:Interest is assumed to be relevant for students' learning processes. Many studies have investigated students' interest in science; most of them however have not offered differentiated insights into the structure and elements of this interest. Purpose:The aim of this study is to obtain a precise image of secondary school students' interest for school and out-of-school learning opportunities, both formal and informal. The study is part of a larger project on measuring the students' Individual Concept about the Natural Sciences (ICoN), including self-efficacy, beliefs and achievements next to interest variables. Sample:Next to regular school students, a specific cohort will be analyzed as well: participants of science competitions who are regarded as having high interest, and perhaps different interest profiles than regular students. In the study described here, participants of the International Junior Science Olympiad (N = 133) and regular students from secondary schools (N = 305), age cohorts 10 to 17 years, participated. Design and methods:We adapted Holland's well-established RIASEC-framework to analyze if and how it can also be used to assess students' interest within science and in-school and out-of-school (leisure-time and enrichment) activities. The resulting questionnaire was piloted according to quality criteria and applied to analyze profiles of different groups (boys - girls, contest participants - non-participants). Results:The RIASEC-adaption to investigate profiles within science works apparently well for school and leisure-time activities. Concerning the interest in fostering measures, different emphases seem to appear. More research in this field needs to be done to adjust measures better to students' interests and other pre-conditions in the future. Contrasting different groups like gender and participation in a junior science contest uncovered specific interest profiles. Conclusions:The instrument seems to offer a promising approach to identify different interest profiles for different environments and groups of students. Based on the results, further studies will be carried out to form a solid foundation for the design of enrichment measures.

Impact of Remedial Reading Interventions on a Secondary Student with Emotional Behavior Disorder: A Case Study

ERIC Educational Resources Information Center

Cooper, LuCinda Nance

2013-01-01

Students who struggle with emotional behavior disorders (EBD) often enter high school with reading levels far below those of their peers. At the secondary level, these at-risk students must regularly read and write proficiently in order to demonstrate their literacy achievement and potential for success either in college or on the job. As a…

Principals' Supervisory Techniques as Correlates of Teachers' Job Performance in Secondary Schools in Ebonyi State, Nigeria

ERIC Educational Resources Information Center

Chidi, Nnebedum; Victor, Akinfolarin Akinwale

2017-01-01

The persistent and prolonged pitiable state of teachers' job performance leading to poor academic achievement of secondary school students in Ebonyi State has become a source of concern and worry among stakeholders and parents. This could be that instructional supervision is not regularly performed by the principals in order to provide…

The Use and Effectiveness of a Question Exploration Routine in Secondary-Level English Language Arts Classrooms

ERIC Educational Resources Information Center

Bulgren, Janis A.; Marquis, Janet G.; Deshler, Donald D.; Lenz, B. Keith; Schumaker, Jean B.

2013-01-01

This purpose of the study was to determine the effects of teachers using the Question Exploration Routine (QER) in regularly scheduled secondary-level English Language Arts classes to help students answer questions about the development and use of main ideas in Shakespeare's "Romeo and Juliet." Questions were posed in both…

Approaches of a Secondary Music Teacher in Response to the Social and Emotional Lives of Students

ERIC Educational Resources Information Center

Edgar, Scott

2015-01-01

Music teachers interact regularly with students experiencing social and emotional challenges and are often under-prepared to do so. The purpose of this study was to examine approaches of a secondary general music teacher in responding to the social and emotional challenges of eight students in a music classroom at an alternative high school. A…

Sample entropy and regularity dimension in complexity analysis of cortical surface structure in early Alzheimer's disease and aging.

PubMed

Chen, Ying; Pham, Tuan D

2013-05-15

We apply for the first time the sample entropy (SampEn) and regularity dimension model for measuring signal complexity to quantify the structural complexity of the brain on MRI. The concept of the regularity dimension is based on the theory of chaos for studying nonlinear dynamical systems, where power laws and entropy measure are adopted to develop the regularity dimension for modeling a mathematical relationship between the frequencies with which information about signal regularity changes in various scales. The sample entropy and regularity dimension of MRI-based brain structural complexity are computed for early Alzheimer's disease (AD) elder adults and age and gender-matched non-demented controls, as well as for a wide range of ages from young people to elder adults. A significantly higher global cortical structure complexity is detected in AD individuals (p<0.001). The increase of SampEn and the regularity dimension are also found to be accompanied with aging which might indicate an age-related exacerbation of cortical structural irregularity. The provided model can be potentially used as an imaging bio-marker for early prediction of AD and age-related cognitive decline. Copyright © 2013 Elsevier B.V. All rights reserved.

The persistence of the attentional bias to regularities in a changing environment.

PubMed

Yu, Ru Qi; Zhao, Jiaying

2015-10-01

The environment often is stable, but some aspects may change over time. The challenge for the visual system is to discover and flexibly adapt to the changes. We examined how attention is shifted in the presence of changes in the underlying structure of the environment. In six experiments, observers viewed four simultaneous streams of objects while performing a visual search task. In the first half of each experiment, the stream in the structured location contained regularities, the shapes in the random location were randomized, and gray squares appeared in two neutral locations. In the second half, the stream in the structured or the random location may change. In the first half of all experiments, visual search was facilitated in the structured location, suggesting that attention was consistently biased toward regularities. In the second half, this bias persisted in the structured location when no change occurred (Experiment 1), when the regularities were removed (Experiment 2), or when new regularities embedded in the original or novel stimuli emerged in the previously random location (Experiments 3 and 6). However, visual search was numerically but no longer reliably faster in the structured location when the initial regularities were removed and new regularities were introduced in the previously random location (Experiment 4), or when novel random stimuli appeared in the random location (Experiment 5). This suggests that the attentional bias was weakened. Overall, the results demonstrate that the attentional bias to regularities was persistent but also sensitive to changes in the environment.

An Algorithm for Protein Helix Assignment Using Helix Geometry

PubMed Central

Cao, Chen; Xu, Shutan; Wang, Lincong

2015-01-01

Helices are one of the most common and were among the earliest recognized secondary structure elements in proteins. The assignment of helices in a protein underlies the analysis of its structure and function. Though the mathematical expression for a helical curve is simple, no previous assignment programs have used a genuine helical curve as a model for helix assignment. In this paper we present a two-step assignment algorithm. The first step searches for a series of bona fide helical curves each one best fits the coordinates of four successive backbone Cα atoms. The second step uses the best fit helical curves as input to make helix assignment. The application to the protein structures in the PDB (protein data bank) proves that the algorithm is able to assign accurately not only regular α-helix but also 310 and π helices as well as their left-handed versions. One salient feature of the algorithm is that the assigned helices are structurally more uniform than those by the previous programs. The structural uniformity should be useful for protein structure classification and prediction while the accurate assignment of a helix to a particular type underlies structure-function relationship in proteins. PMID:26132394

Mentha longifolia syrup in secondary amenorrhea: a double-blind, placebo-controlled, randomized trials

PubMed Central

2012-01-01

Background Amenorrhea is defined as the cessation of menses. Hormone therapy is the most common treatment. Due to the contraindications and side effects of it and the increasing demand for alternative medicine substitutes, Mentha longifolia L. was used in this study. Mentha longifolia L. is a known medication in Iranian traditional medicine to induce menstrual bleeding in women with secondary amenorrhea and oligomenorrhea. Methods A double-blind, randomized, placebo-controlled, multicenter study was conducted in 120 women with secondary amenorrhea and oligomenorrhea. Treatment consisted of sequential oral syrup, 45 ml (15 ml three times a day) for 2 weeks. If the patients did not have menstruation after 2 weeks of taking the medication, we would wait for two more weeks. If the patients had menstruation at each stage of using the drug, we started it one week after the end of menstruation. But if the patients had not menstruate after four weeks (two-week using of drug and waiting for two more weeks), the previous steps were repeated. The drug and placebo were repeated in three cycles of menstruation. Bleeding was documented by the patient on diary cards. The primary outcome variable was the occurrence (yes/no) of bleeding during the first treatment cycle. The secondary efficacy outcome was the regularity of bleeding pattern during the three cycles of the study. Results The number of women with bleeding during the first cycle were higher in the drug group as in the placebo group (68.3% vs. 13.6%; p < 0.001). The regularity of bleeding throughout the study was markedly better in the drug group compared with those given placebo (33.3% vs. 3.3%; p < 0.001). No notable complication or side effect was reported in relation to Mentha longifolia L. syrup. Conclusion In conclusion, Mentha longifolia L. syrup is a safe, well-tolerated, and effective choice in inducing bleeding and maintaining regular bleeding in women with secondary amenorrhea and oligomenorrhea. PMID:23351184

Pi-Pi contacts are an overlooked protein feature relevant to phase separation.

PubMed

Vernon, Robert McCoy; Chong, Paul Andrew; Tsang, Brian; Kim, Tae Hun; Bah, Alaji; Farber, Patrick; Lin, Hong; Forman-Kay, Julie Deborah

2018-02-09

Protein phase separation is implicated in formation of membraneless organelles, signaling puncta and the nuclear pore. Multivalent interactions of modular binding domains and their target motifs can drive phase separation. However, forces promoting the more common phase separation of intrinsically disordered regions are less understood, with suggested roles for multivalent cation-pi, pi-pi, and charge interactions and the hydrophobic effect. Known phase-separating proteins are enriched in pi-orbital containing residues and thus we analyzed pi-interactions in folded proteins. We found that pi-pi interactions involving non-aromatic groups are widespread, underestimated by force-fields used in structure calculations and correlated with solvation and lack of regular secondary structure, properties associated with disordered regions. We present a phase separation predictive algorithm based on pi interaction frequency, highlighting proteins involved in biomaterials and RNA processing. © 2018, Vernon et al.

Three-dimensional electron diffraction of plant light-harvesting complex

PubMed Central

Wang, Da Neng; Kühlbrandt, Werner

1992-01-01

Electron diffraction patterns of two-dimensional crystals of light-harvesting chlorophyll a/b-protein complex (LHC-II) from photosynthetic membranes of pea chloroplasts, tilted at different angles up to 60°, were collected to 3.2 Å resolution at -125°C. The reflection intensities were merged into a three-dimensional data set. The Friedel R-factor and the merging R-factor were 21.8 and 27.6%, respectively. Specimen flatness and crystal size were critical for recording electron diffraction patterns from crystals at high tilts. The principal sources of experimental error were attributed to limitations of the number of unit cells contributing to an electron diffraction pattern, and to the critical electron dose. The distribution of strong diffraction spots indicated that the three-dimensional structure of LHC-II is less regular than that of other known membrane proteins and is not dominated by a particular feature of secondary structure. ImagesFIGURE 1FIGURE 2 PMID:19431817

How the folding rates of two- and multistate proteins depend on the amino acid properties.

PubMed

Huang, Jitao T; Huang, Wei; Huang, Shanran R; Li, Xin

2014-10-01

Proteins fold by either two-state or multistate kinetic mechanism. We observe that amino acids play different roles in different mechanism. Many residues that are easy to form regular secondary structures (α helices, β sheets and turns) can promote the two-state folding reactions of small proteins. Most of hydrophilic residues can speed up the multistate folding reactions of large proteins. Folding rates of large proteins are equally responsive to the flexibility of partial amino acids. Other properties of amino acids (including volume, polarity, accessible surface, exposure degree, isoelectric point, and phase transfer energy) have contributed little to folding kinetics of the proteins. Cysteine is a special residue, it triggers two-state folding reaction and but inhibits multistate folding reaction. These findings not only provide a new insight into protein structure prediction, but also could be used to direct the point mutations that can change folding rate. © 2014 Wiley Periodicals, Inc.

Rethinking "General Audience": A Comparison of Students' Understanding of Popular Film in High School Honors and General-Level Classes

ERIC Educational Resources Information Center

Journell, Wayne; Buchanan, Lisa Brown

2012-01-01

Research suggests that secondary teachers across the United States are regularly turning to popular film as a way to engage students and deliver content. However, research on the use of film in secondary education has yet to focus on how students of varying abilities are able to understand and synthesize academic content when it is presented…

Effects of hand cycle training on physical capacity in individuals with tetraplegia: a clinical trial.

PubMed

Valent, Linda J M; Dallmeijer, Annet J; Houdijk, Han; Slootman, Hans J; Janssen, Thomas W; Post, Marcel W M; van der Woude, Lucas H

2009-10-01

Regular physical activity is important for people with tetraplegia to maintain fitness but may not always be easily integrated into daily life. In many countries, hand cycling has become a serious option for daily mobility in people with tetraplegia. However, little information exists regarding the suitability of this exercise mode for this population. The purpose of this study was to evaluate the effects of a structured hand cycle training program in individuals with chronic tetraplegia. Pretraining and posttraining outcome measurements of physical capacity were compared. Structured hand cycle interval training was conducted at home or in a rehabilitation center in the Netherlands. Twenty-two patients with tetraplegia (American Spinal Injury Association Impairment Scale classification A-D) at least 2 years since injury participated. The intervention was an 8- to 12-week hand cycle interval training program. Primary outcomes of physical capacity were: peak power output (POpeak) and peak oxygen uptake (Vo(2)peak), as determined in hand cycle peak exercise tests on a motor-driven treadmill. Secondary outcome measures were: peak muscle strength (force-generating capacity) of the upper extremities (as assessed by handheld dynamometry), respiratory function (forced vital capacity and peak expiratory flow) and participant-reported shoulder pain. Significant improvements following a mean of 19 (SD=3) sessions of hand cycle training were found in POpeak (from 42.5 W [SD=21.9] to 50.8 W [SD=25.4]), Vo(2)peak (from 1.32 L.min(-1) [SD=0.40] to 1.43 L.min(-1) [SD=0.43]), and mechanical efficiency, as reflected by a decrease in submaximal oxygen uptake. Except for shoulder abduction strength, no significant effects were found on the secondary outcomes. Common health complications, such as urinary tract infections, bowel problems, and pressure sores, led to dropout and nonadherence. Patients with tetraplegia were able to improve their physical capacity through regular hand cycle interval training, without participant-reported shoulder-arm pain or discomfort.

Lymphatics and the breast

MedlinePlus Videos and Cool Tools

... lymphatic system called lymph nodes are distributed at specific locations throughout the body. There is also an ... result in the formation of a secondary cancer mass in a different location of the body. Regular ...

Informed community mobilization for dengue prevention in households with and without a regular water supply: Secondary analysis from the Camino Verde trial in Nicaragua.

PubMed

Cárcamo, Alvaro; Arosteguí, Jorge; Coloma, Josefina; Harris, Eva; Ledogar, Robert J; Andersson, Neil

2017-05-30

Studies in different countries have identified irregular water supply as a risk factor for dengue virus transmission. In 2013, Camino Verde, a cluster-randomised controlled trial in Managua, Nicaragua, and Mexico's Guerrero State, demonstrated impact of evidence-based community mobilisation on recent dengue infection and entomological indexes of infestation by Aedes aegypti mosquitoes. This secondary analysis of data from the trial impact survey asks: (1) what is the importance of regular water supply in neighbourhoods with and without the trial intervention and (2) can community interventions like Camino Verde reasonably exclude households with adequate water supply? Entomological data collected in the dry season of 2013 in intervention and control communities allow contrasts between households with regular and irregular water supplies. Indicators of entomological risk included the House Index and pupa positive household index. Generalised linear mixed models with cluster as a random effect compared households with and without regular water, and households in intervention and control communities. For the House Index, regular water supply was associated with a protection in both intervention households (OR 0.7, 95%CI 0.6-0.9) and control households (OR 0.6, 95%CI 0.5-0.8). For the pupa positive household index, we found a similar protection from regular water supply in intervention households (OR 0.6, 95%CI 0.4-0.8) and control households (OR 0.7, 95%CI 0.5-0.9). The Camino Verde intervention had a similar impact on House Index in households with regular water supply (OR 0.7, 95%CI 0.5-1.0) and irregular water supply (OR 0.6, 95%CI 0.4-0.8); for the pupa positive household index, the effect of the intervention was very similar in households with regular (OR0.5, 95%CI 0.3-0.8) and irregular (OR 0.5, 95%CI 0.3-0.9) water supply. While Aedes aegypti control efforts based on informed community mobilisation had a strong impact on households without a regular water supply, this intervention also impacted entomological indices in households with a regular water supply. These households should not be excluded from community mobilisation efforts to reduce the Aedes aegypti vector. ISRCTN27581154 .

A protein block based fold recognition method for the annotation of twilight zone sequences.

PubMed

Suresh, V; Ganesan, K; Parthasarathy, S

2013-03-01

The description of protein backbone was recently improved with a group of structural fragments called Structural Alphabets instead of the regular three states (Helix, Sheet and Coil) secondary structure description. Protein Blocks is one of the Structural Alphabets used to describe each and every region of protein backbone including the coil. According to de Brevern (2000) the Protein Blocks has 16 structural fragments and each one has 5 residues in length. Protein Blocks fragments are highly informative among the available Structural Alphabets and it has been used for many applications. Here, we present a protein fold recognition method based on Protein Blocks for the annotation of twilight zone sequences. In our method, we align the predicted Protein Blocks of a query amino acid sequence with a library of assigned Protein Blocks of 953 known folds using the local pair-wise alignment. The alignment results with z-value ≥ 2.5 and P-value ≤ 0.08 are predicted as possible folds. Our method is able to recognize the possible folds for nearly 35.5% of the twilight zone sequences with their predicted Protein Block sequence obtained by pb_prediction, which is available at Protein Block Export server.

What secondary science teachers pay attention to in the classroom: Situating teaching in institutional and social systems

NASA Astrophysics Data System (ADS)

Levin, Daniel Matthew

This study concerns the issue of secondary science teachers' attention. In particular, I consider if, how, and when science teachers attend to the substance of student thinking, which is called for by science education reform (NRC, 2007). Using a case study approach, and drawing on ethnographic data sources, I explore what novice and experienced secondary science teachers regularly attend to while teaching, what shapes teachers' attention, and how teachers' attention is consequential for students' science learning. I find that both novice and experienced teachers can attend to the substance of student thinking, although the institutional and social systems of school draw teachers' attention to other foci---particularly to correctness of conceptual knowledge and the vocabulary that signals correctness and "misconceptions." Furthermore, I argue that when teachers regularly attend to the substance of student thinking, they can contribute to a classroom culture that supports student inquiry. I discuss implications of this work for understanding teaching and for teacher education and professional development, and I suggest areas for future research that are motivated by these findings.

77 FR 66838 - Farm Credit Administration Board; Sunshine Act; Regular Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-07

... FURTHER INFORMATION CONTACT: Dale L. Aultman, Secretary to the Farm Credit Administration Board, (703) 883...* Reports Office of Secondary Market Oversight Quarterly Report Dated: November 2, 2012. Dale L. Aultman...

76 FR 26727 - Farm Credit Administration Board; Sunshine Act; Regular Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-09

... business. FOR FURTHER INFORMATION CONTACT: Dale L. Aultman, Secretary to the Farm Credit Administration... Session* Reports Office of Secondary Mortgage Oversight Quarterly Report Dated: May 5, 2011. Dale L...

Elementary Basic Skills Program State Report, Elementary and Secondary Education Act, Title I. Part I--Regular Term 1972-73; Part II--Summer Term 1972.

ERIC Educational Resources Information Center

Maryland State Dept. of Education, Baltimore. Div. of Compensatory, Urban, and Supplementary Programs.

The Elementary Secondary Education Act Title I Elementary Basic Skills program operated in 72 schools during fiscal year 1973. There were approximately 23,443 identified Title I pupils who received the services of the program. The first major program objective pertains directly to reading comprehension and anticipates a gain of ten school months…

Causes of Grade Nine Students' Grade Retention in General Secondary Schools of Dabat Woreda in North Gondar, Ethiopia

ERIC Educational Resources Information Center

Eyasu, Nahom

2017-01-01

One of the great problems of Ethiopia for the educational arena is retention. Averagely 8.07% of each year of the secondary education students is repeated due to lack of achievement in this country. The percentage of retention in a country shows what proportion of students is regularly repeated in the same grade and who are, therefore, committing…

Predicting the Academic Achievement of Deaf and Hard-of-Hearing Students From Individual, Household, Communication, and Educational Factors

PubMed Central

Marschark, Marc; Shaver, Debra M.; Nagle, Katherine M.; Newman, Lynn A.

2015-01-01

Research suggests that the academic achievement of deaf and hard-of-hearing (DHH) students is the result of a complex interplay of many factors. These factors include characteristics of the students (e.g., hearing thresholds, language fluencies, mode of communication, and communication functioning), characteristics of their family environments (e.g., parent education level, socioeconomic status), and experiences inside and outside school (e.g., school placement, having been retained at grade level). This paper examines the relative importance of such characteristics to U.S. DHH secondary students’ academic achievement as indicated by the Woodcock-Johnson III subtests in passage comprehension, mathematics calculation, science, and social studies. Data were obtained for approximately 500 DHH secondary students who had attended regular secondary schools or state-sponsored special schools designed for DHH students. Across all subject areas, having attended regular secondary schools and having better spoken language were associated with higher test scores. Significant negative predictors of achievement varied by type of subtest but included having an additional diagnosis of a learning disability, having a mild hearing loss, and being African American or Hispanic. The findings have important implications for policy and practice in educating DHH students as well for interpreting previous research. PMID:26549890

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

Wemmer, D.E.; Kumar, N.V.; Metrione, R.M.

Toxin II from Radianthus paumotensis (Rp/sub II/) has been investigated by high-resolution NMR and chemical sequencing methods. Resonance assignments have been obtained for this protein by the sequential approach. NMR assignments could not be made consistent with the previously reported primary sequence for this protein, and chemical methods have been used to determine a sequence with which the NMR data are consistent. Analysis of the 2D NOE spectra shows that the protein secondary structure is comprised of two sequences of ..beta..-sheet, probably joined into a distorted continuous sheet, connected by turns and extended loops, without any regular ..cap alpha..-helical segments.more » The residues previously implicated in activity in this class of proteins, D8 and R13, occur in a loop region.« less

Image volume analysis of omnidirectional parallax regular-polyhedron three-dimensional displays.

PubMed

Kim, Hwi; Hahn, Joonku; Lee, Byoungho

2009-04-13

Three-dimensional (3D) displays having regular-polyhedron structures are proposed and their imaging characteristics are analyzed. Four types of conceptual regular-polyhedron 3D displays, i.e., hexahedron, octahedron, dodecahedron, and icosahedrons, are considered. In principle, regular-polyhedron 3D display can present omnidirectional full parallax 3D images. Design conditions of structural factors such as viewing angle of facet panel and observation distance for 3D display with omnidirectional full parallax are studied. As a main issue, image volumes containing virtual 3D objects represented by the four types of regular-polyhedron displays are comparatively analyzed.

Regular intake of non-opioid analgesics is associated with an increased risk of restless legs syndrome in patients maintained on antidepressants.

PubMed

Leutgeb, U; Martus, P

2002-08-30

To evaluate prevalence and risk factors of restless legs syndrome (RLS) in secondary-care patients maintained on tricyclic and serotonin reuptake inhibiting antidepressants. A total of 243 subjects with affective and anxiety disorders were interviewed for symptoms of RLS before and after at least 6 months of antidepressant pharmacotherapy within a naturalistic study. Logistic regression analysis was applied to adjust for the effects of age, gender, comorbidities, and the most frequent co-medications. The overall prevalence of RLS was 27%. In the RLS-affected patients, regular use or overuse of non-opioid analgesics frequently combined with caffeine was the major risk factor which significantly correlated with psychiatric and medical comorbidity. In a subsample of 172 patients who had seldom taken analgesics the prevalence of RLS was 9%, which corresponds with its prevalence in the general population. Neither antidepressants nor neuroleptics but non-opioid analgesics appear to be a major risk factor of RLS. Their regular use should be considered in studies of RLS-patients on psychotropic or other drugs. In this sample of secondary-care patients, ICD-10 classified depression or anxiety per se did not appear to be a risk factor of RLS.

Meta-ecosystem dynamics and functioning on finite spatial networks

PubMed Central

Marleau, Justin N.; Guichard, Frédéric; Loreau, Michel

2014-01-01

The addition of spatial structure to ecological concepts and theories has spurred integration between sub-disciplines within ecology, including community and ecosystem ecology. However, the complexity of spatial models limits their implementation to idealized, regular landscapes. We present a model meta-ecosystem with finite and irregular spatial structure consisting of local nutrient–autotrophs–herbivores ecosystems connected through spatial flows of materials and organisms. We study the effect of spatial flows on stability and ecosystem functions, and provide simple metrics of connectivity that can predict these effects. Our results show that high rates of nutrient and herbivore movement can destabilize local ecosystem dynamics, leading to spatially heterogeneous equilibria or oscillations across the meta-ecosystem, with generally increased meta-ecosystem primary and secondary production. However, the onset and the spatial scale of these emergent dynamics depend heavily on the spatial structure of the meta-ecosystem and on the relative movement rate of the autotrophs. We show how this strong dependence on finite spatial structure eludes commonly used metrics of connectivity, but can be predicted by the eigenvalues and eigenvectors of the connectivity matrix that describe the spatial structure and scale. Our study indicates the need to consider finite-size ecosystems in meta-ecosystem theory. PMID:24403323

Territorial organization of the lowland classic maya.

PubMed

Marcus, J

1973-06-01

Thus far I have discussed ancient Maya sociopolitical structure from the upper levels of the hierarchy downward. Let me now summarize their territorial organization from the bottom upward, starting at the hamlet level (Fig. 8). The smallest unit of settlement-one usually overlooked by archeological surveys in the lowland rain forest-was probably a cluster of thatched huts occupied by a group of related families; larger clusters may have been divided into four quadrants along the lines suggested by Coe (26). Because of the long fallow period (6 to 8 years) characteristic of slash-and-burn agriculture in the Petén, these small hamlets are presumed to have changed location over the years, although they probably shifted in a somewhat circular fashion around a tertiary ceremonial-civic center for whose maintenance they were partly responsible. These tertiary centers were spaced at fairly regular intervals around secondary ceremonial-civic centers with pyramids, carved monuments, and palace-like residences. In turn, the secondary centers occurred at such regular intervals as to form hexagonal patterns around primary centers, which were still larger, with acropolises, multiple ceremonial plazas, and greater numbers of monuments. In some cases, the distance between secondary centers was roughly twice the distance between secondary and tertiary centers, creating a lattice of nested hexagonal cells. This pattern, which conforms to a Western theoretical construct, was presumably caused by factors of service function, travel, and transport. The pattern was not recognized by the Maya at all. They simply recognized that a whole series of smaller centers were dependent on a primary center and therefore mentioned its emblem glyph. Linking the centers of the various hexagons were marriage alliances between members of royal dynasties, who had no kinship ties with the farmers in the hamlets. Out of the large number of primary centers available to them, the Maya selected four as regional capitals. True to their cosmology, the Maya regarded these capitals as associated with the four quadrants of their realm, regardless of their actual location. Each was the home city for a very important dynasty whose junior members probably ruled secondary centers. Since the hexagonal lattices were probably adjusted to variations in population density, each of the four quadrants of the Maya realm probably controlled a comparable number of persons. So strong was the cognized model that, despite the rise and fall of individual centers, there seem always to have been four capitals, each associated with a direction and, presumably, with a color. There is still a great deal to learn about the social, political, and territorial organization of the lowland Maya, and parts of the picture presented here need far more data for their confirmation. What seems likely is that the Maya had an overall quadripartite organization (rather than a core and buffer zone) and that within each quadrant there was at least a five-tiered administrative hierarchy of capital, secondary center, tertiary center, village, and hamlet. Perhaps most significant, there was no real conflict between the lattice-like network predicted by locational analysis and the cosmological four-part structure predicted by epigraphy and ethnology.

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.

Selection of regularization parameter for l1-regularized damage detection

NASA Astrophysics Data System (ADS)

Hou, Rongrong; Xia, Yong; Bao, Yuequan; Zhou, Xiaoqing

2018-06-01

The l1 regularization technique has been developed for structural health monitoring and damage detection through employing the sparsity condition of structural damage. The regularization parameter, which controls the trade-off between data fidelity and solution size of the regularization problem, exerts a crucial effect on the solution. However, the l1 regularization problem has no closed-form solution, and the regularization parameter is usually selected by experience. This study proposes two strategies of selecting the regularization parameter for the l1-regularized damage detection problem. The first method utilizes the residual and solution norms of the optimization problem and ensures that they are both small. The other method is based on the discrepancy principle, which requires that the variance of the discrepancy between the calculated and measured responses is close to the variance of the measurement noise. The two methods are applied to a cantilever beam and a three-story frame. A range of the regularization parameter, rather than one single value, can be determined. When the regularization parameter in this range is selected, the damage can be accurately identified even for multiple damage scenarios. This range also indicates the sensitivity degree of the damage identification problem to the regularization parameter.

Instructors' use of technology in post-secondary undergraduate mathematics teaching: a local study

NASA Astrophysics Data System (ADS)

Jesso, A. T.; Kondratieva, M. F.

2016-02-01

In this study, instructors of undergraduate mathematics from post-secondary institutions in Newfoundland were surveyed (N = 13) and interviewed (N = 8) about their use of, experiences with, and views on, technologically assisted teaching. It was found that the majority of them regularly use technologies for organizational and communication purposes. However, the use of math-specific technology such as computer algebra systems, or dynamic geometry software for instructional, exploratory, and creative activities with students takes place mostly on an individual basis, only occasionally, and is very much topic specific. This was even the case for those instructors who use technology proficiently in their research. The data also suggested that familiarity with and discussions of examples of technology implementation in teaching at regular and field-oriented professional development seminars within mathematics departments could potentially increase the use of math-specific technology by instructors.

How does the Structure of Spherical Dark Matter Halos Affect the Types of Orbits in Disk Galaxies?

NASA Astrophysics Data System (ADS)

Zotos, Euaggelos E.

The main objective of this work is to determine the character of orbits of stars moving in the meridional (R,z) plane of an axially symmetric time-independent disk galaxy model with a central massive nucleus and an additional spherical dark matter halo component. In particular, we try to reveal the influence of the scale length of the dark matter halo on the different families of orbits of stars, by monitoring how the percentage of chaotic orbits, as well as the percentages of orbits of the main regular resonant families evolve when this parameter varies. The smaller alignment index (SALI) was computed by numerically integrating the equations of motion as well as the variational equations to extensive samples of orbits in order to distinguish safely bet ween ordered and chaotic motion. In addition, a method based on the concept of spectral dynamics that utilizes the Fourier transform of the time series of each coordinate is used to identify the various families of regular orbits and also to recognize the secondary resonances that bifurcate from them. Our numerical computations reveal that when the dark matter halo is highly concentrated, that is when the scale length has low values the vast majority of star orbits move in regular orbits, while on the oth er hand in less concentrated dark matter halos the percentage of chaos increases significantly. We also compared our results with early related work.

Infants Prefer the Musical Meter of Their Own Culture: A Cross-Cultural Comparison

ERIC Educational Resources Information Center

Soley, Gaye; Hannon, Erin E.

2010-01-01

Infants prefer native structures such as familiar faces and languages. Music is a universal human activity containing structures that vary cross-culturally. For example, Western music has temporally regular metric structures, whereas music of the Balkans (e.g., Bulgaria, Macedonia, Turkey) can have both regular and irregular structures. We…

An ERP study of regular and irregular English past tense inflection.

PubMed

Newman, Aaron J; Ullman, Michael T; Pancheva, Roumyana; Waligura, Diane L; Neville, Helen J

2007-01-01

Compositionality is a critical and universal characteristic of human language. It is found at numerous levels, including the combination of morphemes into words and of words into phrases and sentences. These compositional patterns can generally be characterized by rules. For example, the past tense of most English verbs ("regulars") is formed by adding an -ed suffix. However, many complex linguistic forms have rather idiosyncratic mappings. For example, "irregular" English verbs have past tense forms that cannot be derived from their stems in a consistent manner. Whether regular and irregular forms depend on fundamentally distinct neurocognitive processes (rule-governed combination vs. lexical memorization), or whether a single processing system is sufficient to explain the phenomena, has engendered considerable investigation and debate. We recorded event-related potentials while participants read English sentences that were either correct or had violations of regular past tense inflection, irregular past tense inflection, syntactic phrase structure, or lexical semantics. Violations of regular past tense and phrase structure, but not of irregular past tense or lexical semantics, elicited left-lateralized anterior negativities (LANs). These seem to reflect neurocognitive substrates that underlie compositional processes across linguistic domains, including morphology and syntax. Regular, irregular, and phrase structure violations all elicited later positivities that were maximal over midline parietal sites (P600s), and seem to index aspects of controlled syntactic processing of both phrase structure and morphosyntax. The results suggest distinct neurocognitive substrates for processing regular and irregular past tense forms: regulars depending on compositional processing, and irregulars stored in lexical memory.

High-speed manufacturing of highly regular femtosecond laser-induced periodic surface structures: physical origin of regularity.

PubMed

Gnilitskyi, Iaroslav; Derrien, Thibault J-Y; Levy, Yoann; Bulgakova, Nadezhda M; Mocek, Tomáš; Orazi, Leonardo

2017-08-16

Highly regular laser-induced periodic surface structures (HR-LIPSS) have been fabricated on surfaces of Mo, steel alloy and Ti at a record processing speed on large areas and with a record regularity in the obtained sub-wavelength structures. The physical mechanisms governing LIPSS regularity are identified and linked with the decay length (i.e. the mean free path) of the excited surface electromagnetic waves (SEWs). The dispersion of the LIPSS orientation angle well correlates with the SEWs decay length: the shorter this length, the more regular are the LIPSS. A material dependent criterion for obtaining HR-LIPSS is proposed for a large variety of metallic materials. It has been found that decreasing the spot size close to the SEW decay length is a key for covering several cm 2 of material surface by HR-LIPSS in a few seconds. Theoretical predictions suggest that reducing the laser wavelength can provide the possibility of HR-LIPSS production on principally any metal. This new achievement in the unprecedented level of control over the laser-induced periodic structure formation makes this laser-writing technology to be flexible, robust and, hence, highly competitive for advanced industrial applications based on surface nanostructuring.

EVOLUTION OF THE IMMUNE RESPONSE

PubMed Central

Papermaster, Ben W.; Condie, Richard M.; Finstad, Joanne; Good, Robert A.

1964-01-01

1. The California hagfish, Eptatretus stoutii, seems to be completely lacking in adaptive immunity: it forms no detectable circulating antibody despite intensive stimulation with a range of antigens; it does not show reactivity to old tuberculin following sensitization with BCG; and gives no evidence of homograft immunity. 2. Studies on the sea lamprey, Petromyzon marinus, have been limited to the response to bacteriophage T2 and hemocyanin in small groups of spawning animals. They suggest that the lamprey may have a low degree of immunologic reactivity. 3. One holostean, the bowfin (Amia calva) and the guitarfish (Rhinobatos productus), an elasmobranch, showed a low level of primary response to phage and hemocyanin. The response is slow and antibody levels low. Both the bowfin and the guitarfish showed a vigorous secondary response to phage, but neither showed much enhancement of reactivity to hemocyanin in the secondary response. The bowfin formed precipitating antibody to hemocyanin, but the guitarfish did not. Both hemagglutinating and precipitating antibody to hemocyanin were also observed in the primary response of the black bass. 4. The bowfin was successfully sensitized to Ascaris antigen, and lesions of the delayed type developed after challenge at varying intervals following sensitization. 5. The horned shark (Heterodontus franciscii) regularly cleared hemocyanin from the circulation after both primary and secondary antigenic stimulation, and regularly formed hemagglutinating antibody, but not precipitating antibody, after both primary and secondary stimulation with this antigen. These animals regularly cleared bacteriophage from the circulation after both the primary and secondary stimulation with bacteriophage T2. Significant but small amounts of antibody were produced in a few animals in the primary response, and larger amounts in the responding animals after secondary antigenic stimulation. 6. Studies by starch gel and immunoelectrophoresis show that the hagfish has no bands with mobilities of mammalian gamma globulins; that the lamprey has a single, relatively faint band of this type; and that multiple gamma bands are characteristic of the holostean, elasmobranchs, and teleosts studied. By this method of study, the bowfin appeared to have substantial amounts of gamma2 globulin. 7. We conclude that adaptive immunity and its cellular and humoral correlates developed in the lowest vertebrates, and that a rising level of immunologic reactivity and an increasingly differentiated and complex immunologic mechanism are observed going up the phylogenetic scale from the hagfish, to the lamprey, to the elasmobranchs, to the holosteans, and finally the teleosts. PMID:14113107

Sparse regularization for EIT reconstruction incorporating structural information derived from medical imaging.

PubMed

Gong, Bo; Schullcke, Benjamin; Krueger-Ziolek, Sabine; Mueller-Lisse, Ullrich; Moeller, Knut

2016-06-01

Electrical impedance tomography (EIT) reconstructs the conductivity distribution of a domain using electrical data on its boundary. This is an ill-posed inverse problem usually solved on a finite element mesh. For this article, a special regularization method incorporating structural information of the targeted domain is proposed and evaluated. Structural information was obtained either from computed tomography images or from preliminary EIT reconstructions by a modified k-means clustering. The proposed regularization method integrates this structural information into the reconstruction as a soft constraint preferring sparsity in group level. A first evaluation with Monte Carlo simulations indicated that the proposed solver is more robust to noise and the resulting images show fewer artifacts. This finding is supported by real data analysis. The structure based regularization has the potential to balance structural a priori information with data driven reconstruction. It is robust to noise, reduces artifacts and produces images that reflect anatomy and are thus easier to interpret for physicians.

Discovering Structural Regularity in 3D Geometry

PubMed Central

Pauly, Mark; Mitra, Niloy J.; Wallner, Johannes; Pottmann, Helmut; Guibas, Leonidas J.

2010-01-01

We introduce a computational framework for discovering regular or repeated geometric structures in 3D shapes. We describe and classify possible regular structures and present an effective algorithm for detecting such repeated geometric patterns in point- or mesh-based models. Our method assumes no prior knowledge of the geometry or spatial location of the individual elements that define the pattern. Structure discovery is made possible by a careful analysis of pairwise similarity transformations that reveals prominent lattice structures in a suitable model of transformation space. We introduce an optimization method for detecting such uniform grids specifically designed to deal with outliers and missing elements. This yields a robust algorithm that successfully discovers complex regular structures amidst clutter, noise, and missing geometry. The accuracy of the extracted generating transformations is further improved using a novel simultaneous registration method in the spatial domain. We demonstrate the effectiveness of our algorithm on a variety of examples and show applications to compression, model repair, and geometry synthesis. PMID:21170292

Early Acceleration of Mathematics Students and its Effect on Growth in Self-esteem: A Longitudinal Study

NASA Astrophysics Data System (ADS)

Ma, Xin

2002-11-01

The Longitudinal Study of American Youth (LSAY) database was employed to examine the educational practice of early acceleration of students of mathematics on the development of their self-esteem across the entire secondary grade levels. Students were classified into three different academic categories (gifted, honors, and regular). Results indicated that, in terms of the development of their self-esteem, gifted students benefited from early acceleration, honors students neither benefited nor were harmed by early acceleration, and regular students were harmed by early acceleration. Early acceleration in mathematics promoted significant growth in self-esteem among gifted male students and among gifted, honors, and regular minority students. When students were accelerated, schools showed similar average growth in self-esteem among gifted students and regular students and a large effect of general support for mathematics on the average growth in self-esteem among honors students.

The yeast Pif1 helicase prevents genomic instability caused by G-quadruplex-forming CEB1 sequences in vivo.

PubMed

Ribeyre, Cyril; Lopes, Judith; Boulé, Jean-Baptiste; Piazza, Aurèle; Guédin, Aurore; Zakian, Virginia A; Mergny, Jean-Louis; Nicolas, Alain

2009-05-01

In budding yeast, the Pif1 DNA helicase is involved in the maintenance of both nuclear and mitochondrial genomes, but its role in these processes is still poorly understood. Here, we provide evidence for a new Pif1 function by demonstrating that its absence promotes genetic instability of alleles of the G-rich human minisatellite CEB1 inserted in the Saccharomyces cerevisiae genome, but not of other tandem repeats. Inactivation of other DNA helicases, including Sgs1, had no effect on CEB1 stability. In vitro, we show that CEB1 repeats formed stable G-quadruplex (G4) secondary structures and the Pif1 protein unwinds these structures more efficiently than regular B-DNA. Finally, synthetic CEB1 arrays in which we mutated the potential G4-forming sequences were no longer destabilized in pif1Delta cells. Hence, we conclude that CEB1 instability in pif1Delta cells depends on the potential to form G-quadruplex structures, suggesting that Pif1 could play a role in the metabolism of G4-forming sequences.

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

Educational career and predictors of type of education in young adults with spina bifida.

PubMed

Barf, H A; Verhoef, M; Post, M W M; Jennekens-Schinkel, A; Gooskens, R H J M; Mullaart, R A; Prevo, A J H

2004-03-01

Children with spina bifida (SB) often require special education. To date, little information is available about the educational career of these children. This study focuses on educational career and predictors of attending special education of young adults with SB, using a cross-sectional study including 178 young Dutch adults with SB aged from 16-25. The main outcome was attending regular versus special education. For searching predictive power we selected age, gender, type of SB, level of lesion, hydrocephalus (HC), number of surgical interventions, ambulation, continence and cognitive functioning. Chi-square tests and binary logistic regression were used in the data analysis. Participants with HC attended special primary education more often (59%) than participants without HC (17%). For those participants with HC, the necessity of special primary education was associated with below average intelligence (75% versus 35%), wheelchair dependence (82% versus 39%) and surgical interventions (74% versus 44%). Only half of the participants with HC followed regular secondary education, whereas for participants with SB without HC, the outcome in secondary education was similar to that of the general population (92%). Intelligence was the main predictor of attending special secondary education (odds 5.1:1), but HC (odds 4.3:1) and wheelchair dependence (odds 2.6:1) were also a significant. Other variables were not significant predictors of special secondary education.

Regular exercise behaviour and intention and symptoms of anxiety and depression in coronary heart disease patients across Europe: Results from the EUROASPIRE III survey.

PubMed

Prugger, Christof; Wellmann, Jürgen; Heidrich, Jan; De Bacquer, Dirk; De Smedt, Delphine; De Backer, Guy; Reiner, Željko; Empana, Jean-Philippe; Fras, Zlatko; Gaita, Dan; Jennings, Catriona; Kotseva, Kornelia; Wood, David; Keil, Ulrich

2017-01-01

Regular exercise lowers the risk of cardiovascular death in coronary heart disease (CHD) patients. We aimed to investigate regular exercise behaviour and intention in relation to symptoms of anxiety and depression in CHD patients across Europe. This study was based on a multicentre cross-sectional survey. In the EUROpean Action on Secondary and Primary Prevention through Intervention to Reduce Events (EUROASPIRE) III survey, 8966 CHD patients <80 years of age from 22 European countries were interviewed on average 15 months after hospitalisation. Whether patients exercised or intended to exercise regularly was assessed using the Stages of Change questionnaire in 8330 patients. Symptoms of anxiety and depression were evaluated using the Hospital Anxiety and Depression Scale. Total physical activity was measured by the International Physical Activity Questionnaire in patients from a subset of 14 countries. Overall, 50.3% of patients were not intending to exercise regularly, 15.9% were intending to exercise regularly, and 33.8% were exercising regularly. Patients with severe symptoms of depression less frequently exercised regularly than patients with symptoms in the normal range (20.2%, 95% confidence interval (CI) 14.8-26.8 vs 36.7%, 95% CI 29.8-44.2). Among patients not exercising regularly, patients with severe symptoms of depression were less likely to have an intention to exercise regularly (odds ratio 0.62, 95% CI 0.46-0.85). Symptoms of anxiety did not affect regular exercise intention. In sensitivity analysis, results were consistent when adjusting for total physical activity. Lower frequency of regular exercise and decreased likelihood of exercise intention were observed in CHD patients with severe depressive symptoms. Severe symptoms of depression may preclude CHD patients from performing regular exercise. © The European Society of Cardiology 2016.

Self-assembly of a binodal metal-organic framework exhibiting a demi-regular lattice.

PubMed

Yan, Linghao; Kuang, Guowen; Zhang, Qiushi; Shang, Xuesong; Liu, Pei Nian; Lin, Nian

2017-10-26

Designing metal-organic frameworks with new topologies is a long-standing quest because new topologies often accompany new properties and functions. Here we report that 1,3,5-tris[4-(pyridin-4-yl)phenyl]benzene molecules coordinate with Cu atoms to form a two-dimensional framework in which Cu adatoms form a nanometer-scale demi-regular lattice. The lattice is articulated by perfectly arranged twofold and threefold pyridyl-Cu coordination motifs in a ratio of 1 : 6 and features local dodecagonal symmetry. This structure is thermodynamically robust and emerges solely when the molecular density is at a critical value. In comparison, we present three framework structures that consist of semi-regular and regular lattices of Cu atoms self-assembled out of 1,3,5-tris[4-(pyridin-4-yl)phenyl]benzene and trispyridylbenzene molecules. Thus a family of regular, semi-regular and demi-regular lattices can be achieved by Cu-pyridyl coordination.

Influencing Factors of the Initiation Point in the Parachute-Bomb Dynamic Detonation System

NASA Astrophysics Data System (ADS)

Qizhong, Li; Ye, Wang; Zhongqi, Wang; Chunhua, Bai

2017-12-01

The parachute system has been widely applied in modern armament design, especially for the fuel-air explosives. Because detonation of fuel-air explosives occurs during flight, it is necessary to investigate the influences of the initiation point to ensure successful dynamic detonation. In fact, the initiating position exist the falling area in the fuels, due to the error of influencing factors. In this paper, the major influencing factors of initiation point were explored with airdrop and the regularity between initiation point area and factors were obtained. Based on the regularity, the volume equation of initiation point area was established to predict the range of initiation point in the fuel. The analysis results showed that the initiation point appeared area, scattered on account of the error of attitude angle, secondary initiation charge velocity, and delay time. The attitude angle was the major influencing factors on a horizontal axis. On the contrary, secondary initiation charge velocity and delay time were the major influencing factors on a horizontal axis. Overall, the geometries of initiation point area were sector coupled with the errors of the attitude angle, secondary initiation charge velocity, and delay time.

Endemic infections are always possible on regular networks

NASA Astrophysics Data System (ADS)

Del Genio, Charo I.; House, Thomas

2013-10-01

We study the dependence of the largest component in regular networks on the clustering coefficient, showing that its size changes smoothly without undergoing a phase transition. We explain this behavior via an analytical approach based on the network structure, and provide an exact equation describing the numerical results. Our work indicates that intrinsic structural properties always allow the spread of epidemics on regular networks.

Electromagnetic Performance Calculation of HTS Linear Induction Motor for Rail Systems

NASA Astrophysics Data System (ADS)

Liu, Bin; Fang, Jin; Cao, Junci; Chen, Jie; Shu, Hang; Sheng, Long

2017-07-01

According to a high temperature superconducting (HTS) linear induction motor (LIM) designed for rail systems, the influence of electromagnetic parameters and mechanical structure parameters on the electromagnetic horizontal thrust, vertical force of HTS LIM and the maximum vertical magnetic field of HTS windings are analyzed. Through the research on the vertical field of HTS windings, the development regularity of the HTS LIM maximum input current with different stator frequency and different thickness value of the secondary conductive plate is obtained. The theoretical results are of great significance to analyze the stability of HTS LIM. Finally, based on theory analysis, HTS LIM test platform was built and the experiment was carried out with load. The experimental results show that the theoretical analysis is correct and reasonable.

A Secondary Antibody-Detecting Molecular Weight Marker with Mouse and Rabbit IgG Fc Linear Epitopes for Western Blot Analysis

PubMed Central

Cheng, Ta-Chun; Tung, Yi-Ching; Chu, Pei-Yu; Chuang, Chih-Hung; Hsieh, Yuan-Chin; Huang, Chien-Chiao; Wang, Yeng-Tseng; Kao, Chien-Han; Roffler, Steve R.; Cheng, Tian-Lu

2016-01-01

Molecular weight markers that can tolerate denaturing conditions and be auto-detected by secondary antibodies offer great efficacy and convenience for Western Blotting. Here, we describe M&R LE protein markers which contain linear epitopes derived from the heavy chain constant regions of mouse and rabbit immunoglobulin G (IgG Fc LE). These markers can be directly recognized and stained by a wide range of anti-mouse and anti-rabbit secondary antibodies. We selected three mouse (M1, M2 and M3) linear IgG1 and three rabbit (R1, R2 and R3) linear IgG heavy chain epitope candidates based on their respective crystal structures. Western blot analysis indicated that M2 and R2 linear epitopes are effectively recognized by anti-mouse and anti-rabbit secondary antibodies, respectively. We fused the M2 and R2 epitopes (M&R LE) and incorporated the polypeptide in a range of 15–120 kDa auto-detecting markers (M&R LE protein marker). The M&R LE protein marker can be auto-detected by anti-mouse and anti-rabbit IgG secondary antibodies in standard immunoblots. Linear regression analysis of the M&R LE protein marker plotted as gel mobility versus the log of the marker molecular weights revealed good linearity with a correlation coefficient R2 value of 0.9965, indicating that the M&R LE protein marker displays high accuracy for determining protein molecular weights. This accurate, regular and auto-detected M&R LE protein marker may provide a simple, efficient and economical tool for protein analysis. PMID:27494183

A Secondary Antibody-Detecting Molecular Weight Marker with Mouse and Rabbit IgG Fc Linear Epitopes for Western Blot Analysis.

PubMed

Lin, Wen-Wei; Chen, I-Ju; Cheng, Ta-Chun; Tung, Yi-Ching; Chu, Pei-Yu; Chuang, Chih-Hung; Hsieh, Yuan-Chin; Huang, Chien-Chiao; Wang, Yeng-Tseng; Kao, Chien-Han; Roffler, Steve R; Cheng, Tian-Lu

2016-01-01

Molecular weight markers that can tolerate denaturing conditions and be auto-detected by secondary antibodies offer great efficacy and convenience for Western Blotting. Here, we describe M&R LE protein markers which contain linear epitopes derived from the heavy chain constant regions of mouse and rabbit immunoglobulin G (IgG Fc LE). These markers can be directly recognized and stained by a wide range of anti-mouse and anti-rabbit secondary antibodies. We selected three mouse (M1, M2 and M3) linear IgG1 and three rabbit (R1, R2 and R3) linear IgG heavy chain epitope candidates based on their respective crystal structures. Western blot analysis indicated that M2 and R2 linear epitopes are effectively recognized by anti-mouse and anti-rabbit secondary antibodies, respectively. We fused the M2 and R2 epitopes (M&R LE) and incorporated the polypeptide in a range of 15-120 kDa auto-detecting markers (M&R LE protein marker). The M&R LE protein marker can be auto-detected by anti-mouse and anti-rabbit IgG secondary antibodies in standard immunoblots. Linear regression analysis of the M&R LE protein marker plotted as gel mobility versus the log of the marker molecular weights revealed good linearity with a correlation coefficient R2 value of 0.9965, indicating that the M&R LE protein marker displays high accuracy for determining protein molecular weights. This accurate, regular and auto-detected M&R LE protein marker may provide a simple, efficient and economical tool for protein analysis.

Regularized Generalized Structured Component Analysis

ERIC Educational Resources Information Center

Hwang, Heungsun

2009-01-01

Generalized structured component analysis (GSCA) has been proposed as a component-based approach to structural equation modeling. In practice, GSCA may suffer from multi-collinearity, i.e., high correlations among exogenous variables. GSCA has yet no remedy for this problem. Thus, a regularized extension of GSCA is proposed that integrates a ridge…

What Information Does Your EHR Contain? Automatic Generation of a Clinical Metadata Warehouse (CMDW) to Support Identification and Data Access Within Distributed Clinical Research Networks.

PubMed

Bruland, Philipp; Doods, Justin; Storck, Michael; Dugas, Martin

2017-01-01

Data dictionaries provide structural meta-information about data definitions in health information technology (HIT) systems. In this regard, reusing healthcare data for secondary purposes offers several advantages (e.g. reduce documentation times or increased data quality). Prerequisites for data reuse are its quality, availability and identical meaning of data. In diverse projects, research data warehouses serve as core components between heterogeneous clinical databases and various research applications. Given the complexity (high number of data elements) and dynamics (regular updates) of electronic health record (EHR) data structures, we propose a clinical metadata warehouse (CMDW) based on a metadata registry standard. Metadata of two large hospitals were automatically inserted into two CMDWs containing 16,230 forms and 310,519 data elements. Automatic updates of metadata are possible as well as semantic annotations. A CMDW allows metadata discovery, data quality assessment and similarity analyses. Common data models for distributed research networks can be established based on similarity analyses.

CRF: detection of CRISPR arrays using random forest.

PubMed

Wang, Kai; Liang, Chun

2017-01-01

CRISPRs (clustered regularly interspaced short palindromic repeats) are particular repeat sequences found in wide range of bacteria and archaea genomes. Several tools are available for detecting CRISPR arrays in the genomes of both domains. Here we developed a new web-based CRISPR detection tool named CRF (CRISPR Finder by Random Forest). Different from other CRISPR detection tools, a random forest classifier was used in CRF to filter out invalid CRISPR arrays from all putative candidates and accordingly enhanced detection accuracy. In CRF, particularly, triplet elements that combine both sequence content and structure information were extracted from CRISPR repeats for classifier training. The classifier achieved high accuracy and sensitivity. Moreover, CRF offers a highly interactive web interface for robust data visualization that is not available among other CRISPR detection tools. After detection, the query sequence, CRISPR array architecture, and the sequences and secondary structures of CRISPR repeats and spacers can be visualized for visual examination and validation. CRF is freely available at http://bioinfolab.miamioh.edu/crf/home.php.

Sequence-specific sup 1 H NMR resonance assignments of Bacillus subtilis HPr: Use of spectra obtained from mutants to resolve spectral overlap

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

Wittekind, M.; Klevit, R.E.; Reizer, J.

1990-08-07

On the basis of an analysis of two-dimensional {sup 1}H NMR spectra, the complete sequence-specific {sup 1}H NMR assignments are presented for the phosphocarrier protein HPr from the Gram-positive bacterium Bacillus subtilis. During the assignment procedure, extensive use was made of spectra obtained from point mutants of HPr in order to resolve spectral overlap and to provide verification of assignments. Regions of regular secondary structure were identified by characteristic patterns of sequential backbone proton NOEs and slowly exchanging amide protons. B subtilis HPr contains four {beta}-strands that form a single antiparallel {beta}-sheet and two well-defined {alpha}-helices. There are two stretchesmore » of extended backbone structure, one of which contains the active site His{sub 15}. The overall fold of the protein is very similar to that of Escherichia coli HPr determined by NMR studies.« less

Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families.

PubMed

Reinharz, Vladimir; Soulé, Antoine; Westhof, Eric; Waldispühl, Jérôme; Denise, Alain

2018-05-04

The wealth of the combinatorics of nucleotide base pairs enables RNA molecules to assemble into sophisticated interaction networks, which are used to create complex 3D substructures. These interaction networks are essential to shape the 3D architecture of the molecule, and also to provide the key elements to carry molecular functions such as protein or ligand binding. They are made of organised sets of long-range tertiary interactions which connect distinct secondary structure elements in 3D structures. Here, we present a de novo data-driven approach to extract automatically from large data sets of full RNA 3D structures the recurrent interaction networks (RINs). Our methodology enables us for the first time to detect the interaction networks connecting distinct components of the RNA structure, highlighting their diversity and conservation through non-related functional RNAs. We use a graphical model to perform pairwise comparisons of all RNA structures available and to extract RINs and modules. Our analysis yields a complete catalog of RNA 3D structures available in the Protein Data Bank and reveals the intricate hierarchical organization of the RNA interaction networks and modules. We assembled our results in an online database (http://carnaval.lri.fr) which will be regularly updated. Within the site, a tool allows users with a novel RNA structure to detect automatically whether the novel structure contains previously observed RINs.

Comprehensive computational design of ordered peptide macrocycles

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

Hosseinzadeh, Parisa; Bhardwaj, Gaurav; Mulligan, Vikram Khipple

Mixed chirality peptide macrocycles such as cyclosporine are among the most potent therapeutics identified to-date, but there is currently no way to systematically search through the structural space spanned by such compounds for new drug candidates. Natural proteins do not provide a useful guide: peptide macrocycles lack regular secondary structures and hydrophobic cores and have different backbone torsional constraints. Hence the development of new peptide macrocycles has been approached by modifying natural products or using library selection methods; the former is limited by the small number of known structures, and the latter by the limited size and diversity accessible throughmore » library-based methods. To overcome these limitations, here we enumerate the stable structures that can be adopted by macrocyclic peptides composed of L and D amino acids. We identify more than 200 designs predicted to fold into single stable structures, many times more than the number of currently available unbound peptide macrocycle structures. We synthesize and characterize by NMR twelve 7-10 residue macrocycles, 9 of which have structures very close to the design models in solution. NMR structures of three 11-14 residue bicyclic designs are also very close to the computational models. Our results provide a nearly complete coverage of the rich space of structures possible for short peptide based macrocycles unparalleled for other molecular systems, and vastly increase the available starting scaffolds for both rational drug design and library selection methods.« less

29 CFR 541.303 - Teachers.

Code of Federal Regulations, 2012 CFR

2012-07-01

... public schools are not uniform in requiring a certificate for employment as an elementary or secondary...: Regular academic teachers; teachers of kindergarten or nursery school pupils; teachers of gifted or... activities are a recognized part of the schools' responsibility in contributing to the educational...

29 CFR 541.303 - Teachers.

Code of Federal Regulations, 2014 CFR

2014-07-01

... public schools are not uniform in requiring a certificate for employment as an elementary or secondary...: Regular academic teachers; teachers of kindergarten or nursery school pupils; teachers of gifted or... activities are a recognized part of the schools' responsibility in contributing to the educational...

29 CFR 541.303 - Teachers.

Code of Federal Regulations, 2013 CFR

2013-07-01

... public schools are not uniform in requiring a certificate for employment as an elementary or secondary...: Regular academic teachers; teachers of kindergarten or nursery school pupils; teachers of gifted or... activities are a recognized part of the schools' responsibility in contributing to the educational...

Measuring Attitudes toward Inclusive Education.

ERIC Educational Resources Information Center

Wilczenski, Felicia L.

1992-01-01

Developed scale to measure attitudes toward inclusive education, in which disabled students are responsibility of regular teacher supported by specialists. Administered scale to 301 elementary and secondary teachers and to 144 undergraduate elementary education majors. Analysis yielded four discrete dimensions of inclusive education with…

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/.

Secondary pigmentary glaucoma in patients with underlying primary pigment dispersion syndrome.

PubMed

Sivaraman, Kavitha R; Patel, Chirag G; Vajaranant, Thasarat S; Aref, Ahmad A

2013-01-01

Primary pigment dispersion syndrome (PPDS) is a bilateral condition that occurs in anatomically predisposed individuals. PPDS may evolve into pigmentary glaucoma, but it is difficult to predict which patients will progress. Secondary pigment dispersion is more often unilateral and acquired as a result of surgery, trauma, or intraocular tumor, but can likewise lead to pigmentary glaucoma. We report two cases of patients with bilateral PPDS who developed secondary pigment dispersion and pigmentary glaucoma in one eye. Patients with PPDS who acquire a secondary mechanism of pigment dispersion may be at an increased risk of progression to pigmentary glaucoma, presumably due to an increased burden of liberated pigment. In addition to regular surveillance for progression to glaucoma from PPDS, secondary causes of pigmentary dispersion in these eyes should be considered when patients present with grossly asymmetric findings. When secondary pigment dispersion is identified in eyes with PPDS, we recommend prompt intervention to alleviate the cause of secondary pigment dispersion and/or aggressive control of intraocular pressure to limit glaucomatous damage.

Secondary pigmentary glaucoma in patients with underlying primary pigment dispersion syndrome

PubMed Central

Sivaraman, Kavitha R; Patel, Chirag G; Vajaranant, Thasarat S; Aref, Ahmad A

2013-01-01

Primary pigment dispersion syndrome (PPDS) is a bilateral condition that occurs in anatomically predisposed individuals. PPDS may evolve into pigmentary glaucoma, but it is difficult to predict which patients will progress. Secondary pigment dispersion is more often unilateral and acquired as a result of surgery, trauma, or intraocular tumor, but can likewise lead to pigmentary glaucoma. We report two cases of patients with bilateral PPDS who developed secondary pigment dispersion and pigmentary glaucoma in one eye. Patients with PPDS who acquire a secondary mechanism of pigment dispersion may be at an increased risk of progression to pigmentary glaucoma, presumably due to an increased burden of liberated pigment. In addition to regular surveillance for progression to glaucoma from PPDS, secondary causes of pigmentary dispersion in these eyes should be considered when patients present with grossly asymmetric findings. When secondary pigment dispersion is identified in eyes with PPDS, we recommend prompt intervention to alleviate the cause of secondary pigment dispersion and/or aggressive control of intraocular pressure to limit glaucomatous damage. PMID:23569351

[Which organization for the management of thoracic cancer? Results from a French survey in Rhône-Alpes region].

PubMed

Couraud, S; Fournel, P; Moro-Sibilot, D; Pérol, M; Souquet, P-J

2012-02-01

This survey, conducted in Rhône-Alpes region (France), aims to better understand the actual conditions of practice in thoracic oncology. A questionnaire was distributed to all oncologists, pulmonologists, radiotherapy physicians and thoracic surgeons in the region. Of 401 questionnaires, the response rate was 56%. Among the responders 46% reported exercising the Thoracic Oncology (TO). Most physicians practicing TO are pulmonologists (62%). The majority (45%) are engaged in secondary hospital or university hospital (27%). However, practitioners with the most important activity exerts in university hospitals and cancer centre (71% of physicians practicing in secondary hospitals and 75% of those in private practice reported to manage fewer than 80 new NSCLC cases per year in structure). Furthermore, 91% are regularly involved in a multidisciplinary team. Radiation oncologist, pulmonologists and thoracic surgeons are assiduous to these meeting; however radiologists and, to a lesser extent, pathologists are less attentive. Moreover, 92% of practitioners belong to cancer networks. Similarly, over one third of working together in a cooperative clinical research institution and nearly half are involved in clinical trials (with nearly half in secondary hospital). These results highlight the reality of practice in Rhône-Alpes and will serve as the basis for coordinating authorities to correct dysfunctions or monitor certain activities of interest (clinical trials). Copyright © 2011 Elsevier Masson SAS. All rights reserved.

Vocational Guidance in Secondary Education: A Report of the Commission on the Reorganization of Secondary Education Appointed by the National Education Association. Bulletin, 1918, No. 19

ERIC Educational Resources Information Center

Bureau of Education, Department of the Interior, 1918

1918-01-01

In no other country in the world do so many boys and girls receive regular high-school education of a general cultural type as in the United States, and the number of such boys and girls in this country is rapidly increasing, having more than doubled since 1905, and increased more than 60 per cent since 1910. American democratic ideals demand not…

Chinese Children's Statistical Learning of Orthographic Regularities: Positional Constraints and Character Structure

ERIC Educational Resources Information Center

Tong, Xiuli; McBride, Catherine

2014-01-01

This study examined how Chinese children acquire the untaught positional constraints of stroke patterns that are embedded in left-right structured and top-bottom structured characters. Using an orthographic regularity pattern elicitation paradigm, 536 Hong Kong Chinese children at different levels of reading (kindergarten, 2nd, and 5th grades)…

Orientation determination of interfacial beta-sheet structures in situ.

PubMed

Nguyen, Khoi Tan; King, John Thomas; Chen, Zhan

2010-07-01

Structural information such as orientations of interfacial proteins and peptides is important for understanding properties and functions of such biological molecules, which play crucial roles in biological applications and processes such as antimicrobial selectivity, membrane protein activity, biocompatibility, and biosensing performance. The alpha-helical and beta-sheet structures are the most widely encountered secondary structures in peptides and proteins. In this paper, for the first time, a method to quantify the orientation of the interfacial beta-sheet structure using a combined attenuated total reflectance Fourier transformation infrared spectroscopic (ATR-FTIR) and sum frequency generation (SFG) vibrational spectroscopic study was developed. As an illustration of the methodology, the orientation of tachyplesin I, a 17 amino acid peptide with an antiparallel beta-sheet, adsorbed to polymer surfaces as well as associated with a lipid bilayer was determined using the regular and chiral SFG spectra, together with polarized ATR-FTIR amide I signals. Both the tilt angle (theta) and the twist angle (psi) of the beta-sheet at interfaces are determined. The developed method in this paper can be used to obtain in situ structural information of beta-sheet components in complex molecules. The combination of this method and the existing methodology that is currently used to investigate alpha-helical structures will greatly broaden the application of optical spectroscopy in physical chemistry, biochemistry, biophysics, and structural biology.

Multiple graph regularized protein domain ranking.

PubMed

Wang, Jim Jing-Yan; Bensmail, Halima; Gao, Xin

2012-11-19

Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods. To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods. The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications.

Multiple graph regularized protein domain ranking

PubMed Central

2012-01-01

Background Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods. Results To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods. Conclusion The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications. PMID:23157331

The 1997 IDEA Amendments: Implications for School Principals.

ERIC Educational Resources Information Center

Williams, Brenda T.; Katsiyannis, Antonis

1998-01-01

Discusses implications of the 1997 Individuals with Disabilities Education Act Amendments for local policy and practice. Secondary principals should understand new requirements for locating and evaluating eligible students with disabilities, including disabled students in state and districtwide assessment programs, involving regular teachers in…

Hidden Markov model approach for identifying the modular framework of the protein backbone.

PubMed

Camproux, A C; Tuffery, P; Chevrolat, J P; Boisvieux, J F; Hazout, S

1999-12-01

The hidden Markov model (HMM) was used to identify recurrent short 3D structural building blocks (SBBs) describing protein backbones, independently of any a priori knowledge. Polypeptide chains are decomposed into a series of short segments defined by their inter-alpha-carbon distances. Basically, the model takes into account the sequentiality of the observed segments and assumes that each one corresponds to one of several possible SBBs. Fitting the model to a database of non-redundant proteins allowed us to decode proteins in terms of 12 distinct SBBs with different roles in protein structure. Some SBBs correspond to classical regular secondary structures. Others correspond to a significant subdivision of their bounding regions previously considered to be a single pattern. The major contribution of the HMM is that this model implicitly takes into account the sequential connections between SBBs and thus describes the most probable pathways by which the blocks are connected to form the framework of the protein structures. Validation of the SBBs code was performed by extracting SBB series repeated in recoding proteins and examining their structural similarities. Preliminary results on the sequence specificity of SBBs suggest promising perspectives for the prediction of SBBs or series of SBBs from the protein sequences.

Consistent Partial Least Squares Path Modeling via Regularization.

PubMed

Jung, Sunho; Park, JaeHong

2018-01-01

Partial least squares (PLS) path modeling is a component-based structural equation modeling that has been adopted in social and psychological research due to its data-analytic capability and flexibility. A recent methodological advance is consistent PLS (PLSc), designed to produce consistent estimates of path coefficients in structural models involving common factors. In practice, however, PLSc may frequently encounter multicollinearity in part because it takes a strategy of estimating path coefficients based on consistent correlations among independent latent variables. PLSc has yet no remedy for this multicollinearity problem, which can cause loss of statistical power and accuracy in parameter estimation. Thus, a ridge type of regularization is incorporated into PLSc, creating a new technique called regularized PLSc. A comprehensive simulation study is conducted to evaluate the performance of regularized PLSc as compared to its non-regularized counterpart in terms of power and accuracy. The results show that our regularized PLSc is recommended for use when serious multicollinearity is present.

Homework and Science Learning in Secondary Schools.

ERIC Educational Resources Information Center

Tamir, Pinchas

1985-01-01

Offers a conceptual framework for studying and analyzing potential benefits/disadvantages of homework. Also describes studies (measurement of conditions, practices, and attitudes toward homework). Findings show that students value homework, that few teachers regularly check homework, and that there are sex differences between Arab and Jewish…

Microcomputer Programs for Health Occupations Education. A Bibliography.

ERIC Educational Resources Information Center

Florida State Univ., Tallahassee. Center for Instructional Development and Services.

This annotated bibliography describes materials available for computer-assisted instruction in secondary and postsecondary health and allied health programs. The materials are suitable for use by regular, disadvantaged, and handicapped students and by students whose facility in English is limited. The bibliography includes software programs…

Working with the Disadvantaged Student in Vocational Education.

ERIC Educational Resources Information Center

DeKalb SERVE Satellite Center, Stone Mountain, GA.

This handbook provides vocational educators at the secondary and postsecondary levels with approaches for working with minimally disadvantaged students enrolled in their regular programs. Chapter 1 focuses on the disadvantaged student and considers such problems as perceptual difficulties, resistance to authority, parental influence, insecurity…

Hypocalcemia and tetany caused by vitamin D deficiency in a child with intestinal lymphangiectasia.

PubMed

Lu, Ying-Yi; Wu, Jia-Feng; Ni, Yen-Hsuan; Peng, Steven Shinn-Forng; Shun, Chia-Tung; Chang, Mei-Hwei

2009-10-01

Primary intestinal lymphangiectasia is a rare disease of children, which is characterized by chronic diarrhea and complicated with malnutrition, including fat-soluble vitamin deficiency. We report a girl aged 4 years and 8 months who was diagnosed with the disease by endoscopic duodenal biopsy at 8 months of age. She presented initially with chronic diarrhea at 4 months of age. Generalized edema with hypoalbuminemia frequently occurred despite regular albumin supplements. Multiple vitamins initially were not supplied regularly. Episodes of tetany caused by hypocalcemia developed 4 years after the diagnosis of intestinal lymphangiectasia. Imaging study (long-bone X-ray and dual-energy X-ray absorptiometry) revealed low bone density. Complicated vitamin D deficiency [low serum 25-hydroxy vitamin D concentration (< 12.48 mmol/L, the detection limit)] and secondary hyperparathyroidism were confirmed via blood testing. Vitamin D supplementation for 3 months improved her bone density, secondary hyperparathyroidism and frequent tetany. Vitamin D status should be monitored in patients with intestinal lymphangiectasia.

Modeling of ETL-Processes and Processed Information in Clinical Data Warehousing.

PubMed

Tute, Erik; Steiner, Jochen

2018-01-01

Literature describes a big potential for reuse of clinical patient data. A clinical data warehouse (CDWH) is a means for that. To support management and maintenance of processes extracting, transforming and loading (ETL) data into CDWHs as well as to ease reuse of metadata between regular IT-management, CDWH and secondary data users by providing a modeling approach. Expert survey and literature review to find requirements and existing modeling techniques. An ETL-modeling-technique was developed extending existing modeling techniques. Evaluation by exemplarily modeling existing ETL-process and a second expert survey. Nine experts participated in the first survey. Literature review yielded 15 included publications. Six existing modeling techniques were identified. A modeling technique extending 3LGM² and combining it with openEHR information models was developed and evaluated. Seven experts participated in the evaluation. The developed approach can help in management and maintenance of ETL-processes and could serve as interface between regular IT-management, CDWH and secondary data users.

[Secondary impingement syndrome in athletes].

PubMed

Jerosch, J; Castro, W H; Sons, H U

1990-12-01

Dysfunction of the shoulder joint is based not only on anatomic conditions. The consideration of the special kinesiology of the shoulder helps to understand the shoulder pathology. This mainly applies to young "overhead athletes" like swimmers, handball-, basketball-, volleyball-, and racketplayers. These disciplines cause stress on the anterior joint structures (capsule, ligaments, labrum, subscapularis tendon) and lead to anterior instability. This includes anterior subluxation or even dislocation. Finally, an impingement syndrome with the typical symptoms can frequently result from these conditions. The impingement-syndrome of the elderly must be considered as a primary disease, whereas the young overhead athlete suffers from the impingement syndrome as a secondary disease and does not take the first place in therapy. The first step in therapy should to be treat the muscular imbalance of the shoulder. To gain a regular pattern of motion the rotator cuff must be strengthened. This regimen is likely to be successful in 80-90% of the cases. If the conservative therapy fails the surgical treatment may come into consideration. Arthroscopic surgery has the advantage not to affect the proprioceptivity. To retain the previous level of performance an adequate rehabilitation programme is essential for the athlete.

Human action recognition with group lasso regularized-support vector machine

NASA Astrophysics Data System (ADS)

Luo, Huiwu; Lu, Huanzhang; Wu, Yabei; Zhao, Fei

2016-05-01

The bag-of-visual-words (BOVW) and Fisher kernel are two popular models in human action recognition, and support vector machine (SVM) is the most commonly used classifier for the two models. We show two kinds of group structures in the feature representation constructed by BOVW and Fisher kernel, respectively, since the structural information of feature representation can be seen as a prior for the classifier and can improve the performance of the classifier, which has been verified in several areas. However, the standard SVM employs L2-norm regularization in its learning procedure, which penalizes each variable individually and cannot express the structural information of feature representation. We replace the L2-norm regularization with group lasso regularization in standard SVM, and a group lasso regularized-support vector machine (GLRSVM) is proposed. Then, we embed the group structural information of feature representation into GLRSVM. Finally, we introduce an algorithm to solve the optimization problem of GLRSVM by alternating directions method of multipliers. The experiments evaluated on KTH, YouTube, and Hollywood2 datasets show that our method achieves promising results and improves the state-of-the-art methods on KTH and YouTube datasets.

Regularized matrix regression

PubMed Central

Zhou, Hua; Li, Lexin

2014-01-01

Summary Modern technologies are producing a wealth of data with complex structures. For instance, in two-dimensional digital imaging, flow cytometry and electroencephalography, matrix-type covariates frequently arise when measurements are obtained for each combination of two underlying variables. To address scientific questions arising from those data, new regression methods that take matrices as covariates are needed, and sparsity or other forms of regularization are crucial owing to the ultrahigh dimensionality and complex structure of the matrix data. The popular lasso and related regularization methods hinge on the sparsity of the true signal in terms of the number of its non-zero coefficients. However, for the matrix data, the true signal is often of, or can be well approximated by, a low rank structure. As such, the sparsity is frequently in the form of low rank of the matrix parameters, which may seriously violate the assumption of the classical lasso. We propose a class of regularized matrix regression methods based on spectral regularization. A highly efficient and scalable estimation algorithm is developed, and a degrees-of-freedom formula is derived to facilitate model selection along the regularization path. Superior performance of the method proposed is demonstrated on both synthetic and real examples. PMID:24648830

Electronic-cigarette use among young people in Wales: evidence from two cross-sectional surveys

PubMed Central

Moore, Graham; Hewitt, Gillian; Evans, John; Littlecott, Hannah J; Holliday, Jo; Ahmed, Nilufar; Moore, Laurence; Murphy, Simon; Fletcher, Adam

2015-01-01

Objectives To examine the prevalence of electronic(e)-cigarette use, prevalence of e-cigarette and tobacco use by age, and associations of e-cigarette use with sociodemographic characteristics, tobacco and cannabis use among young people in Wales. Design Data from two nationally-representative cross-sectional surveys undertaken in 2013–2014. Logistic regression analyses, adjusting for school-level clustering, examined sociodemographic characteristics of e-cigarette use, and associations between e-cigarette use and smoking. Setting Primary and secondary schools in Wales. Participants Primary-school children aged 10–11 (n=1601) and secondary-school students aged 11–16 (n=9055). Results Primary-school children were more likely to have used e-cigarettes (5.8%) than tobacco (1.6%). Ever use of e-cigarettes remained more prevalent than ever use of tobacco until age 14–15. Overall, 12.3% of secondary-school students (aged 11–16) reported ever using e-cigarettes, with no differences according to gender, ethnicity or family affluence. The percentage of ‘never smokers’ reporting having used e-cigarettes was 5.3% at age 10–11 to 8.0% at age 15–16. The proportion of children who had ever used an e-cigarette and reported currently smoking increased from 6.9% among 10–11 year olds to 39.2% in 15–16 year olds. Only 1.5% (n=125) of 11–16 year-olds, including 0.3% of never smokers, reported regular e-cigarette use (use at least once a month). Current weekly smokers were 100 times more likely than non-smokers to report regular e-cigarette use (relative risk ratio (RRR=121.15; 95% CI 57.56 to 254.97). Regular e-cigarette use was also more likely among those who had smoked cannabis (RRR 53.03; 95% CI 38.87 to 80.65). Conclusions Many young people (including never-smokers) have tried e-cigarettes. However, regular use is less common, and is associated with tobacco cigarette use. Longitudinal research is needed to understand age-related trajectories of e-cigarette use and to understand the temporal nature of relationships between e-cigarette and tobacco use. PMID:25877272

Inputs from regularly and irregularly discharging vestibular nerve afferents to secondary neurons in squirrel monkey vestibular nuclei. III. Correlation with vestibulospinal and vestibuloocular output pathways

NASA Technical Reports Server (NTRS)

Boyle, R.; Goldberg, J. M.; Highstein, S. M.

1992-01-01

1. A previous study measured the relative contributions made by regularly and irregularly discharging afferents to the monosynaptic vestibular nerve (Vi) input of individual secondary neurons located in and around the superior vestibular nucleus of barbiturate-anesthetized squirrel monkeys. Here, the analysis is extended to more caudal regions of the vestibular nuclei, which are a major source of both vestibuloocular and vestibulospinal pathways. As in the previous study, antidromic stimulation techniques are used to classify secondary neurons as oculomotor or spinal projecting. In addition, spinal-projecting neurons are distinguished by their descending pathways, their termination levels in the spinal cord, and their collateral projections to the IIIrd nucleus. 2. Monosynaptic excitatory postsynaptic potentials (EPSPs) were recorded intracellularly from secondary neurons as shocks of increasing strength were applied to Vi. Shocks were normalized in terms of the threshold (T) required to evoke field potentials in the vestibular nuclei. As shown previously, the relative contribution of irregular afferents to the total monosynaptic Vi input of each secondary neuron can be expressed as a %I index, the ratio (x100) of the relative sizes of the EPSPs evoked by shocks of 4 x T and 16 x T. 3. Antidromic stimulation was used to type secondary neurons as 1) medial vestibulospinal tract (MVST) cells projecting to spinal segments C1 or C6; 2) lateral vestibulospinal tract (LVST) cells projecting to C1, C6; or L1; 3) vestibulooculo-collic (VOC) cells projecting both to the IIIrd nucleus and by way of the MVST to C1 or C6; and 4) vestibuloocular (VOR) neurons projecting to the IIIrd nucleus but not to the spinal cord. Most of the neurons were located in the lateral vestibular nucleus (LV), including its dorsal (dLV) and ventral (vLV) divisions, and adjacent parts of the medial (MV) and descending nuclei (DV). Cells receiving quite different proportions of their direct inputs from regular and irregular afferents were intermingled in all regions explored. 4. LVST neurons are restricted to LV and DV and show a somatotopic organization. Those destined for the cervical and thoracic cord come from vLV, from a transition zone between vLV and DV, and to a lesser extent from dLV. Lumbar-projecting neurons are located more dorsally in dLV and more caudally in DV. MVST neurons reside in MV and in the vLV-DV transition zone.(ABSTRACT TRUNCATED AT 400 WORDS).

Structural and Functional Characterization of the Recombinant Death Domain from Death-Associated Protein Kinase

PubMed Central

Dioletis, Evangelos; Dingley, Andrew J.; Driscoll, Paul C.

2013-01-01

Death-associated protein kinase (DAPk) is a calcium/calmodulin-regulated Ser/Thr-protein kinase that functions at an important point of integration for cell death signaling pathways. DAPk has a structurally unique multi-domain architecture, including a C-terminally positioned death domain (DD) that is a positive regulator of DAPk activity. In this study, recombinant DAPk-DD was observed to aggregate readily and could not be prepared in sufficient yield for structural analysis. However, DAPk-DD could be obtained as a soluble protein in the form of a translational fusion protein with the B1 domain of streptococcal protein G. In contrast to other DDs that adopt the canonical six amphipathic α-helices arranged in a compact fold, the DAPk-DD was found to possess surprisingly low regular secondary structure content and an absence of a stable globular fold, as determined by circular dichroism (CD), NMR spectroscopy and a temperature-dependent fluorescence assay. Furthermore, we measured the in vitro interaction between extracellular-regulated kinase-2 (ERK2) and various recombinant DAPk-DD constructs. Despite the low level of structural order, the recombinant DAPk-DD retained the ability to interact with ERK2 in a 1∶1 ratio with a K d in the low micromolar range. Only the full-length DAPk-DD could bind ERK2, indicating that the apparent ‘D-motif’ located in the putative sixth helix of DAPk-DD is not sufficient for ERK2 recognition. CD analysis revealed that binding of DAPk-DD to ERK2 is not accompanied by a significant change in secondary structure. Taken together our data argue that the DAPk-DD, when expressed in isolation, does not adopt a classical DD fold, yet in this state retains the capacity to interact with at least one of its binding partners. The lack of a stable globular structure for the DAPk-DD may reflect either that its folding would be supported by interactions absent in our experimental set-up, or a limitation in the structural bioinformatics assignment of the three-dimensional structure. PMID:23922916

Structural and functional characterization of the recombinant death domain from death-associated protein kinase.

PubMed

Dioletis, Evangelos; Dingley, Andrew J; Driscoll, Paul C

2013-01-01

Death-associated protein kinase (DAPk) is a calcium/calmodulin-regulated Ser/Thr-protein kinase that functions at an important point of integration for cell death signaling pathways. DAPk has a structurally unique multi-domain architecture, including a C-terminally positioned death domain (DD) that is a positive regulator of DAPk activity. In this study, recombinant DAPk-DD was observed to aggregate readily and could not be prepared in sufficient yield for structural analysis. However, DAPk-DD could be obtained as a soluble protein in the form of a translational fusion protein with the B1 domain of streptococcal protein G. In contrast to other DDs that adopt the canonical six amphipathic α-helices arranged in a compact fold, the DAPk-DD was found to possess surprisingly low regular secondary structure content and an absence of a stable globular fold, as determined by circular dichroism (CD), NMR spectroscopy and a temperature-dependent fluorescence assay. Furthermore, we measured the in vitro interaction between extracellular-regulated kinase-2 (ERK2) and various recombinant DAPk-DD constructs. Despite the low level of structural order, the recombinant DAPk-DD retained the ability to interact with ERK2 in a 1∶1 ratio with a K d in the low micromolar range. Only the full-length DAPk-DD could bind ERK2, indicating that the apparent 'D-motif' located in the putative sixth helix of DAPk-DD is not sufficient for ERK2 recognition. CD analysis revealed that binding of DAPk-DD to ERK2 is not accompanied by a significant change in secondary structure. Taken together our data argue that the DAPk-DD, when expressed in isolation, does not adopt a classical DD fold, yet in this state retains the capacity to interact with at least one of its binding partners. The lack of a stable globular structure for the DAPk-DD may reflect either that its folding would be supported by interactions absent in our experimental set-up, or a limitation in the structural bioinformatics assignment of the three-dimensional structure.

Long-term effectiveness of a combined student-parent and a student-only smoking prevention intervention among 7th grade school children in Berlin, Germany.

PubMed

Krist, Lilian; Lotz, Fabian; Bürger, Christin; Ströbele-Benschop, Nanette; Roll, Stephanie; Rieckmann, Nina; Müller-Nordhorn, Jacqueline; Willich, Stefan N; Müller-Riemenschneider, Falk

2016-12-01

In Germany, the smoking prevalence among adolescents is among the highest in Europe. Our aim was to evaluate the long-term effectiveness of a combined student-parent and a student-only smoking prevention programme to reduce the smoking prevalence among 7th grade students in Berlin. Three-armed cluster-randomized controlled trial (RCT). Schools as cluster units were randomized into (i) student intervention, (ii) combined student-parent intervention or (iii) control group, with follow-up after 12 and 24 months. High schools and integrated secondary schools in Berlin, Germany. Seventh grade students aged 11-16 years. We included 47 schools, 161 classes and 2801 students [50.1% girls, mean age ± standard deviation (SD) = 13.0 ± 0.6 years]. The primary outcome was self-reported regular smoking (at least one cigarette per day) after 24 months (point prevalence). Further self-reported outcomes were other smoking behaviours as well as parental rules and attitudes towards smoking. Comparisons were calculated as odds ratios (OR) with 95% confidence intervals (CI). At baseline, 2.3% of the students reported that they smoked regularly. After 24 months, 7.8% and 7.0% were regular smokers in the student-only intervention and the student-parent intervention, respectively, compared with 10.1% in the control group. The OR for being a regular smoker was 0.81 (0.34-1.92) for the student-parent intervention versus control, 0.95 (CI = 0.41-2.22) for the student-only intervention versus control and 0.85 (0.38-1.89) for student-parent intervention versus student-only intervention. A combined student-parent smoking prevention intervention delivered via secondary schools in Berlin, Germany did not result in a statistically significant reduction in regular smoking compared with a control group or a student-only intervention. The student-only intervention did not result in a significant reduction in regular smoking compared with the control group. © 2016 Society for the Study of Addiction.

Slow relaxation in weakly open rational polygons.

PubMed

Kokshenev, Valery B; Vicentini, Eduardo

2003-07-01

The interplay between the regular (piecewise-linear) and irregular (vertex-angle) boundary effects in nonintegrable rational polygonal billiards (of m equal sides) is discussed. Decay dynamics in polygons (of perimeter P(m) and small opening Delta) is analyzed through the late-time survival probability S(m) approximately equal t(-delta). Two distinct slow relaxation channels are established. The primary universal channel exhibits relaxation of regular sliding orbits, with delta=1. The secondary channel is given by delta>1 and becomes open when m>P(m)/Delta. It originates from vertex order-disorder dual effects and is due to relaxation of chaoticlike excitations.

AN ERP STUDY OF REGULAR AND IRREGULAR ENGLISH PAST TENSE INFLECTION

PubMed Central

Newman, Aaron J.; Ullman, Michael T.; Pancheva, Roumyana; Waligura, Diane L.; Neville, Helen J.

2006-01-01

Compositionality is a critical and universal characteristic of human language. It is found at numerous levels, including the combination of morphemes into words and of words into phrases and sentences. These compositional patterns can generally be characterized by rules. For example, the past tense of most English verbs (“regulars”) is formed by adding an -ed suffix. However, many complex linguistic forms have rather idiosyncratic mappings. For example, “irregular” English verbs have past tense forms that cannot be derived from their stems in a consistent manner. Whether regular and irregular forms depend on fundamentally distinct neurocognitive processes (rule-governed combination vs. lexical memorization), or whether a single processing system is sufficient to explain the phenomena, has engendered considerable investigation and debate. We recorded event-related potentials while participants read English sentences that were either correct or had violations of regular past tense inflection, irregular past tense inflection, syntactic phrase structure, or lexical semantics. Violations of regular past tense and phrase structure, but not of irregular past tense or lexical semantics, elicited left-lateralized anterior negativities (LANs). These seem to reflect neurocognitive substrates that underlie compositional processes across linguistic domains, including morphology and syntax. Regular, irregular, and phrase structure violations all elicited later positivities that were maximal over right parietal sites (P600s), and which seem to index aspects of controlled syntactic processing of both phrase structure and morphosyntax. The results suggest distinct neurocognitive substrates for processing regular and irregular past tense forms: regulars depending on compositional processing, and irregulars stored in lexical memory. PMID:17070703

Regularity and dimensional salience in temporal grouping.

PubMed

Prince, Jon B; Rice, Tim

2018-04-30

How do pitch and duration accents combine to influence the perceived grouping of musical sequences? Sequence context influences the relative importance of these accents; for example, the presence of learned structure in pitch exaggerates the effect of pitch accents at the expense of duration accents despite being irrelevant to the task and not attributable to attention (Prince, 2014b). In the current study, two experiments examined whether the presence of temporal structure has the opposite effect. Experiment 1 tested baseline conditions, in which participants (N = 30) heard sequences with various sizes of either pitch or duration accents, which implied either duple or triple groupings (accent every two or three notes, respectively). Sequences either had regular temporal structure (isochronous) or not (irregular, via using random interonset intervals). Regularity enhanced the effect of duration accents but had negligible influence on pitch accents. The accent sizes that gave the most equivalent ratings across dimension and regularity levels were used in Experiment 2 (N = 33), in which sequences contained both pitch and duration accents that suggested either duple, triple, or neutral groupings. Despite controlling for the baseline effect of regularity by selecting equally effective accent sizes, regularity had additional effects on duration accents, but only for duple groupings. Regularity did not influence the effectiveness of pitch accents when combined with duration accents. These findings offer some support for a dimensional salience hypothesis, which proposes that the presence of temporal structure should foster duration accent effectiveness at the expense of pitch accents. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

The LBT experience of adaptive secondary mirror operations for routine seeing- and diffraction-limited science operations

NASA Astrophysics Data System (ADS)

Guerra, J. C.; Brusa, G.; Christou, J.; Miller, D.; Ricardi, A.; Xompero, M.; Briguglio, R.; Wagner, M.; Lefebvre, M.; Sosa, R.

2013-09-01

The Large Binocular Telescope (LBT) is unique in that it is currently the only large telescope (2 x 8.4m primary mirrors) with permanently mounted adaptive secondary mirrors (ASMs). These ASMs have been used for regular observing since early 2010 on the right side and since late 2011 on the left side. They are currently regularly used for seeing-limited observing as well as for selective diffraction-limited observing and are required to be fully operational every observing night. By comparison the other telescopes using ASMs, the Multi Mirrot Telescope (MMT) and more recently Magellan, use fixed secondaries of seeing-limited observing and switch in the ASMs for diffraction-limited observing. We will discuss the night-to-night operational requirements for ASMs specifically for seeing-limited but also for diffraction-limited observations based on the LBT experience. These will include preparation procedures for observing (mirror flattening and resting as examples); hardware failure statistics and how to deal with them such as for the actuators; observing protocols for; and current limitations of use due to the ASM technology such as the minimum elevation limit (25 degrees) and the hysteresis of the gravity-vector induced astigmatism. We will also discuss the impact of ASM maintenance and preparation

Structure-Based Low-Rank Model With Graph Nuclear Norm Regularization for Noise Removal.

PubMed

Ge, Qi; Jing, Xiao-Yuan; Wu, Fei; Wei, Zhi-Hui; Xiao, Liang; Shao, Wen-Ze; Yue, Dong; Li, Hai-Bo

2017-07-01

Nonlocal image representation methods, including group-based sparse coding and block-matching 3-D filtering, have shown their great performance in application to low-level tasks. The nonlocal prior is extracted from each group consisting of patches with similar intensities. Grouping patches based on intensity similarity, however, gives rise to disturbance and inaccuracy in estimation of the true images. To address this problem, we propose a structure-based low-rank model with graph nuclear norm regularization. We exploit the local manifold structure inside a patch and group the patches by the distance metric of manifold structure. With the manifold structure information, a graph nuclear norm regularization is established and incorporated into a low-rank approximation model. We then prove that the graph-based regularization is equivalent to a weighted nuclear norm and the proposed model can be solved by a weighted singular-value thresholding algorithm. Extensive experiments on additive white Gaussian noise removal and mixed noise removal demonstrate that the proposed method achieves a better performance than several state-of-the-art algorithms.

The writing approaches of secondary students.

PubMed

Lavelle, Ellen; Smith, Jennifer; O'Ryan, Leslie

2002-09-01

Research with college students has supported a model of writing approaches that defines the relationship between a writer and writing task along a deep and surface process continuum (Biggs, 1988). Based on that model, Lavelle (1993) developed the Inventory of Processes in College Composition which reflects students' motives and strategies as related to writing outcomes. It is also important to define the approaches of secondary students to better understand writing processes at that level, and development in written composition. This study was designed to define the writing approaches of secondary students by factor analysing students' responses to items regarding writing beliefs and writing strategies, and to compare the secondary approaches to those of college students. A related goal was to explore the relationships of the secondary writing approaches to perceived self-regulatory efficacy for writing (Zimmerman & Bandura, 1994), writing preferences, and writing outcomes. The initial, factor analytic phase involved 398 junior level high school students (11th grade) enrolled in a mandatory language arts class at each of three large Midwestern high schools (USA). Then, 49 junior level students enrolled in two language arts classes participated as subjects in the second phase. Classroom teachers administered the Inventory of Processes in College Composition (Lavelle, 1993), which contained 72 true-or-false items regarding writing beliefs and strategies, during regular class periods. Data were factor analysed and the structure compared to that of college students. In the second phase, the new inventory, Inventory of Processes in Secondary Composition, was administered in conjunction with the Perceived Self-Regulatory Efficacy for Writing Inventory (Zimmerman & Bandura, 1994), and a writing preferences survey. A writing sample and grade in Language Arts classes were obtained and served as outcome variables. The factor structure of secondary writing reflected three process dimensions. The first factor, Elaborative-Expressive, describes a writing strategy based on personal investment and audience concern. The second factor, Planful-Procedural, denotes sticking to a plan, following the rules, and 'preparing' for writing. Achieving-Competitive, the third factor, reflects a 'teacher pleasing' strategy or doing only what needs to be done to get a good grade. Two factors from the college model, Elaborative and Procedural, were replicated, and two were not, Reflective-Revision and Low Self-Efficacy. Regression analyses supported that the processes in writing under a timed condition are different from those used when writing over time, and that students' perceptions of writing self-regulatory efficacy were predictive of writing success under both conditions.

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

Waterpipe tobacco smoking prevalence and illegal underage use in waterpipe-serving premises: a cross-sectional analysis among schoolchildren in Stoke-on-Trent.

PubMed

Jawad, M; McIver, C

2017-05-01

Waterpipe tobacco smoking has received little epidemiological and policy attention in the UK despite reports of increasing prevalence alongside an anecdotally non-compliant industry. This study aimed to determine how waterpipe tobacco smoking is changing among young people in the UK, both in terms of prevalence and sociodemographic correlates of use, and to quantify the extent of illegal underage use in waterpipe-serving premises in the UK. Repeat cross-sectional. A secondary analysis of two cross-sectional surveys (total N = 3376), conducted in 2013 and 2015 among secondary school students aged 11-16 years in Stoke-on-Trent, measured lifetime (both surveys) and regular (at least monthly; 2015 survey only) waterpipe tobacco prevalence and location of usual use. Logistic regression models measured the association between independent variables (age, sex, ethnicity, presence of free school meals, cigarette smoking status) with lifetime and regular waterpipe tobacco use, and with illegal underage use; the latter defined as usually smoking waterpipe tobacco in a waterpipe-serving premise. Lifetime waterpipe tobacco prevalence remained similar in 2013 (13.7%, 95% confidence interval [CI] 12.0-15.4%) and 2015 (14.6%, 95% CI 12.8-16.4%), whereas regular use was measured at 2.9% (95% CI 2.1-3.8%) in 2015. Older, non-white, males who concurrently used cigarettes had higher odds of lifetime waterpipe tobacco use. Illegal underage use was reported among 27.1% of all regular users, correlates of which included increasing age and South Asian ethnicity. The presence of free school meals was not associated with lifetime or regular waterpipe tobacco prevalence, nor illegal underage use. Increased monitoring of waterpipe tobacco prevalence and patterns, including the underage policy compliance of waterpipe-serving premises, is needed to help inform policy decisions to control waterpipe tobacco use. Copyright © 2017 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

Molecular identification and characterization of clustered regularly interspaced short palindromic repeat (CRISPR) gene cluster in Taylorella equigenitalis.

PubMed

Hara, Yasushi; Hayashi, Kyohei; Nakajima, Takuya; Kagawa, Shizuko; Tazumi, Akihiro; Moore, John E; Matsuda, Motoo

2013-09-01

Clustered regularly interspaced short palindromic repeats (CRISPRs), of approximately 10,000 base pairs (bp) in length, were shown to occur in the Japanese Taylorella equigenitalis strain, EQ59. The locus was composed of the putative CRISPRs-associated with 5 (cas5), RAMP csd1, csd2, recB, cas1, a leader region, 13 CRISPR consensus sequence repeats (each 32 bp; 5'-TCAGCCACGTTCGCGTGGCTGTGTGTTTAAAG-3'). These were in turn separated by 12 non repetitive unique spacer regions of similar length. In addition, a leader region, a transposase/IS protein, a leader region, and cas3 were also seen. All seven putative open reading frames carry their ribosome binding sites. Promoter consensus sequences at the -35 and -10 regions and putative intrinsic ρ-independent transcription terminator regions also occurred. A possible long overlap of 170 bp in length occurred between the recB and cas1 loci. Positive reverse transcription PCR signals of cas5, RAMP csd1, csd2-recB/cas1, and cas3 were generated. A putative secondary structure of the CRISPR consensus repeats was constructed. Following this, CRISPR results of the T. equigenitalis EQ59 isolate were subsequently compared with those from the Taylorella asinigenitalis MCE3 isolate.

An Accommodations Model for the Secondary Inclusive Classroom

ERIC Educational Resources Information Center

Scanlon, David; Baker, Diana

2012-01-01

Despite expectations for accommodations in inclusive classrooms, little guidance for effective practice is available. Most accommodations policies and evidence-based practices address assessments. High school regular and special educators collaborated in focus groups to articulate a model based on their practices and perceptions of best practice.…

77 FR 46658 - Proposed Priority; Technical Assistance To Improve State Data Capacity-National Technical...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-06

... percent of youth with individualized education programs (IEPs) graduating with a regular high school... 100,000 schools through EDFacts. \\4\\ Education Department General Administrative Regulations (EDGAR... Department programs (e.g., Consolidated State Performance Report under the Elementary and Secondary Education...

Geostatistical regularization operators for geophysical inverse problems on irregular meshes

NASA Astrophysics Data System (ADS)

Jordi, C.; Doetsch, J.; Günther, T.; Schmelzbach, C.; Robertsson, J. OA

2018-05-01

Irregular meshes allow to include complicated subsurface structures into geophysical modelling and inverse problems. The non-uniqueness of these inverse problems requires appropriate regularization that can incorporate a priori information. However, defining regularization operators for irregular discretizations is not trivial. Different schemes for calculating smoothness operators on irregular meshes have been proposed. In contrast to classical regularization constraints that are only defined using the nearest neighbours of a cell, geostatistical operators include a larger neighbourhood around a particular cell. A correlation model defines the extent of the neighbourhood and allows to incorporate information about geological structures. We propose an approach to calculate geostatistical operators for inverse problems on irregular meshes by eigendecomposition of a covariance matrix that contains the a priori geological information. Using our approach, the calculation of the operator matrix becomes tractable for 3-D inverse problems on irregular meshes. We tested the performance of the geostatistical regularization operators and compared them against the results of anisotropic smoothing in inversions of 2-D surface synthetic electrical resistivity tomography (ERT) data as well as in the inversion of a realistic 3-D cross-well synthetic ERT scenario. The inversions of 2-D ERT and seismic traveltime field data with geostatistical regularization provide results that are in good accordance with the expected geology and thus facilitate their interpretation. In particular, for layered structures the geostatistical regularization provides geologically more plausible results compared to the anisotropic smoothness constraints.

Cryptic tRNAs in chaetognath mitochondrial genomes.

PubMed

Barthélémy, Roxane-Marie; Seligmann, Hervé

2016-06-01

The chaetognaths constitute a small and enigmatic phylum of little marine invertebrates. Both nuclear and mitochondrial genomes have numerous originalities, some phylum-specific. Until recently, their mitogenomes seemed containing only one tRNA gene (trnMet), but a recent study found in two chaetognath mitogenomes two and four tRNA genes. Moreover, apparently two conspecific mitogenomes have different tRNA gene numbers (one and two). Reanalyses by tRNAscan-SE and ARWEN softwares of the five available complete chaetognath mitogenomes suggest numerous additional tRNA genes from different types. Their total number never reaches the 22 found in most other invertebrates using that genetic code. Predicted error compensation between codon-anticodon mismatch and tRNA misacylation suggests translational activity by tRNAs predicted solely according to secondary structure for tRNAs predicted by tRNAscan-SE, not ARWEN. Numbers of predicted stop-suppressor (antitermination) tRNAs coevolve with predicted overlapping, frameshifted protein coding genes including stop codons. Sequence alignments in secondary structure prediction with non-chaetognath tRNAs suggest that the most likely functional tRNAs are in intergenic regions, as regular mt-tRNAs. Due to usually short intergenic regions, generally tRNA sequences partially overlap with flanking genes. Some tRNA pairs seem templated by sense-antisense strands. Moreover, 16S rRNA genes, but not 12S rRNAs, appear as tRNA nurseries, as previously suggested for multifunctional ribosomal-like protogenomes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Thermal depth profiling of vascular lesions: automated regularization of reconstruction algorithms

NASA Astrophysics Data System (ADS)

Verkruysse, Wim; Choi, Bernard; Zhang, Jenny R.; Kim, Jeehyun; Nelson, J. Stuart

2008-03-01

Pulsed photo-thermal radiometry (PPTR) is a non-invasive, non-contact diagnostic technique used to locate cutaneous chromophores such as melanin (epidermis) and hemoglobin (vascular structures). Clinical utility of PPTR is limited because it typically requires trained user intervention to regularize the inversion solution. Herein, the feasibility of automated regularization was studied. A second objective of this study was to depart from modeling port wine stain PWS, a vascular skin lesion frequently studied with PPTR, as strictly layered structures since this may influence conclusions regarding PPTR reconstruction quality. Average blood vessel depths, diameters and densities derived from histology of 30 PWS patients were used to generate 15 randomized lesion geometries for which we simulated PPTR signals. Reconstruction accuracy for subjective regularization was compared with that for automated regularization methods. The objective regularization approach performed better. However, the average difference was much smaller than the variation between the 15 simulated profiles. Reconstruction quality depended more on the actual profile to be reconstructed than on the reconstruction algorithm or regularization method. Similar, or better, accuracy reconstructions can be achieved with an automated regularization procedure which enhances prospects for user friendly implementation of PPTR to optimize laser therapy on an individual patient basis.

Energy drinks, soft drinks, and substance use among United States secondary school students.

PubMed

Terry-McElrath, Yvonne M; OʼMalley, Patrick M; Johnston, Lloyd D

2014-01-01

Examine energy drink/shot and regular and diet soft drink use among United States secondary school students in 2010-2011, and associations between such use and substance use. We used self-reported data from cross-sectional surveys of nationally representative samples of 8th-, 10th-, and 12th-grade students and conducted multivariate analyses examining associations between beverage and substance use, controlling for individual and school characteristics. Approximately 30% of students reported consuming energy drinks or shots; more than 40% reported daily regular soft drink use, and about 20% reported daily diet soft drink use. Beverage consumption was strongly and positively associated with past 30-day alcohol, cigarette, and illicit drug use. The observed associations between energy drinks and substance use were significantly stronger than those between regular or diet soft drinks and substance use. This correlational study indicates that adolescent consumption of energy drinks/shots is widespread and that energy drink users report heightened risk for substance use. This study does not establish causation between the behaviors. Education for parents and prevention efforts among adolescents should include education on the masking effects of caffeine in energy drinks on alcohol- and other substance-related impairments, and recognition that some groups (such as high sensation-seeking youth) may be particularly likely to consume energy drinks and to be substance users.

Energy drinks, soft drinks, and substance use among US secondary school students

PubMed Central

Terry-McElrath, Yvonne M.; O’Malley, Patrick M.; Johnston, Lloyd D.

2014-01-01

Objectives Examine energy drink/shot and regular and diet soft drink use among US secondary school students in 2010–2011, and associations between such use and substance use. Methods We used self-reported data from cross-sectional surveys of nationally representative samples of 8th, 10th, and 12th grade students and conducted multivariate analyses examining associations between beverage and substance use controlling for individual and school characteristics. Results Approximately 30% of students reported consuming energy drinks or shots; more than 40% reported daily regular soft drink use, and about 20% reported daily diet soft drink use. Beverage consumption was strongly and positively associated with past 30-day alcohol, cigarette, and illicit drug use. The observed associations between energy drinks and substance use were significantly stronger than those between regular or diet soft drinks and substance use. Conclusions This correlational study indicates that adolescent consumption of energy drinks/shots is wide-spread, and that energy drink users report heightened risk for substance use. This study does not establish causation between the behaviors. Education for parents and prevention efforts among adolescents should include education on the masking effects of caffeine in energy drinks on alcohol- and other substance-related impairments, and recognition that some groups (such as high sensation-seeking youth) may be particularly likely to consume energy drinks and to be substance users. PMID:24481080

USE OF STROKE SECONDARY PREVENTION SERVICES

PubMed Central

Ross, Joseph S.; Halm, Ethan A.; Bravata, Dawn M.

2009-01-01

Objective To examine whether there are disparities in use of stroke secondary prevention services because disparities in stroke outcomes have been found among older adults, women, racial minorities, and within Stroke Belt states. Methods Using the nationally-representative 2005 Behavior Risk Factor Surveillance System, we examined self-reported use of 11 stroke secondary prevention services queried in the survey. We used multivariable logistic regression to examine the association between service use and age, sex, race, and Stroke Belt state residence, controlling for other socio-demographic and health care access characteristics. Results Among 11,862 adults with a history of stroke, 16% were 80 or older, 54% were women, 13% were non-Hispanic black, and 23% lived within a Stroke Belt state. Overall service use varied: 31% reported post-stroke outpatient rehabilitation, 57% regular exercise, 66% smoking cessation counseling, and 91% current use of anti-hypertensive medications. Age 80 or older was not associated with lower use of any of the 11 services. Women were less likely to report post-stroke outpatient rehabilitation and regular exercise when compared with men (P values ≤ 0.005); there were no sex-based differences in use of the 9 other services. Blacks were less likely to report pneumococcal vaccination when compared with whites, but were more likely to report post-stroke outpatient rehabilitation (P values ≤ 0.005); there were no race-based differences in use of the 9 other services. Stroke Belt state residence was not associated with lower use of any of the 11 services. Conclusions Use of many stroke secondary prevention services was suboptimal. We did not find consistent age, sex, racial, or Stroke Belt state residence disparities in care. CONDENSED ABSTRACT We examined the association between stroke secondary prevention service use and age, sex, race, and Stroke Belt state residence using nationally-representative data. Although use of many stroke secondary prevention services was suboptimal, we did not find consistent age, sex, racial, or Stroke Belt state residence disparities in care. PMID:19265044

Effective field theory dimensional regularization

NASA Astrophysics Data System (ADS)

Lehmann, Dirk; Prézeau, Gary

2002-01-01

A Lorentz-covariant regularization scheme for effective field theories with an arbitrary number of propagating heavy and light particles is given. This regularization scheme leaves the low-energy analytic structure of Greens functions intact and preserves all the symmetries of the underlying Lagrangian. The power divergences of regularized loop integrals are controlled by the low-energy kinematic variables. Simple diagrammatic rules are derived for the regularization of arbitrary one-loop graphs and the generalization to higher loops is discussed.

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.

Genomic structure of two ras family genes in the slime mold Physarum polycephalum.

PubMed

Trzcińska-Danielewicz, Joanna; Kozlowski, Piotr; Gierdal, Katarzyna; Wiejak, Jolanta; Jagielski, Adam; Toczko, Kazimierz; Fronk, Jan

2002-08-01

Genomic structure of two Physarum polycephalum ras family genes, Ppras2 and Pprap1, has been determined, including the upstream region of the latter. The genes are interrupted by three and four introns, respectively. The first intron of Ppras2 has the same location within the coding sequence as the first intron in another ras homolog from this organism, Ppras1 [Trzcińska-Danielewicz, J., Kozlowski, P., and Toczko, K. (1996). "Cloning and genomic sequence of the Physarum polycephalum Ppras1 gene, a homologue of the ras protooncogene", Gene 169, pp. 143-144]. All introns, ranging from 53 to ca. 460 base pairs, have the canonical 5' and 3' ends, are greatly enriched in pyrimidines in the coding strand and have frequent pyrimidines-only tracts. These latter features seem to be responsible for the difficulties in cloning and sequencing of parts of these genes. Short sequences shared with P. polycephalum transposon-like repeats are common in the introns, indicating a possible role of transposition in intron evolution. In all three ras family genes phase zero introns are located mostly between sequences coding for regular protein secondary structure elements.

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

Structural characterization of the packings of granular regular polygons.

PubMed

Wang, Chuncheng; Dong, Kejun; Yu, Aibing

2015-12-01

By using a recently developed method for discrete modeling of nonspherical particles, we simulate the random packings of granular regular polygons with three to 11 edges under gravity. The effects of shape and friction on the packing structures are investigated by various structural parameters, including packing fraction, the radial distribution function, coordination number, Voronoi tessellation, and bond-orientational order. We find that packing fraction is generally higher for geometrically nonfrustrated regular polygons, and can be increased by the increase of edge number and decrease of friction. The changes of packing fraction are linked with those of the microstructures, such as the variations of the translational and orientational orders and local configurations. In particular, the free areas of Voronoi tessellations (which are related to local packing fractions) can be described by log-normal distributions for all polygons. The quantitative analyses establish a clearer picture for the packings of regular polygons.

Factors associated with regular physical exercise and consumption of fruits and vegetables among Mexican older adults.

PubMed

Doubova, Svetlana V; Sánchez-García, Sergio; Infante-Castañeda, Claudia; Pérez-Cuevas, Ricardo

2016-09-09

To analyze the factors associated with regular physical exercise and routine consumption of fruits and vegetables, and both healthy behaviors among Mexican older adults. We conducted a secondary data analysis of the baseline data (2014) of the Study on Obesity, Sarcopenia and Fragility in older adults affiliated with the Mexican Institute of Social Security. The study included 948 adults who were ≥60 years of age. Multiple Poisson regression was performed. Routine consumption of fruits and vegetables was reported by 53.8 % of older adults, 42.7 % reported engaging in regular physical exercise and 23.1 % reported participating in both types of healthy behaviors. Women, adults with a stable income, those with a self-perception of good health and those with a history of physical exercise at the age of 50 years had an increased likelihood of engaging in healthy eating and regular physical activity. Many older adults do not routinely consume fruits and vegetables or engage in regular physical exercise despite the fact that most have a fixed income and a social network. It is relevant to conduct research-based interventions that take into account the contextual factors to promote healthy behaviors.

A pragmatic, phase III, multisite, double-blind, placebo-controlled, parallel-arm, dose increment randomised trial of regular, low-dose extended-release morphine for chronic breathlessness: Breathlessness, Exertion And Morphine Sulfate (BEAMS) study protocol.

PubMed

Currow, David; Watts, Gareth John; Johnson, Miriam; McDonald, Christine F; Miners, John O; Somogyi, Andrew A; Denehy, Linda; McCaffrey, Nicola; Eckert, Danny J; McCloud, Philip; Louw, Sandra; Lam, Lawrence; Greene, Aine; Fazekas, Belinda; Clark, Katherine C; Fong, Kwun; Agar, Meera R; Joshi, Rohit; Kilbreath, Sharon; Ferreira, Diana; Ekström, Magnus

2017-07-17

Chronic breathlessness is highly prevalent and distressing to patients and families. No medication is registered for its symptomatic reduction. The strongest evidence is for regular, low-dose, extended- release (ER) oral morphine. A recent large phase III study suggests the subgroup most likely to benefit have chronic obstructive pulmonary disease (COPD) and modified Medical Research Council breathlessness scores of 3 or 4. This protocol is for an adequately powered, parallel-arm, placebo-controlled, multisite, factorial, block-randomised study evaluating regular ER morphine for chronic breathlessness in people with COPD. The primary question is what effect regular ER morphine has on worst breathlessness, measured daily on a 0-10 numerical rating scale. Uniquely, the coprimary outcome will use a FitBit to measure habitual physical activity. Secondary questions include safety and, whether upward titration after initial benefit delivers greater net symptom reduction. Substudies include longitudinal driving simulation, sleep, caregiver, health economic and pharmacogenetic studies. Seventeen centres will recruit 171 participants from respiratory and palliative care. The study has five phases including three randomisation phases to increasing doses of ER morphine. All participants will receive placebo or active laxatives as appropriate. Appropriate statistical analysis of primary and secondary outcomes will be used. Ethics approval has been obtained. Results of the study will be submitted for publication in peer-reviewed journals, findings presented at relevant conferences and potentially used to inform registration of ER morphine for chronic breathlessness. NCT02720822; Pre-results. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

A pragmatic, phase III, multisite, double-blind, placebo-controlled, parallel-arm, dose increment randomised trial of regular, low-dose extended-release morphine for chronic breathlessness: Breathlessness, Exertion And Morphine Sulfate (BEAMS) study protocol

PubMed Central

Watts, Gareth John; Johnson, Miriam; McDonald, Christine F; Miners, John O; Somogyi, Andrew A; Denehy, Linda; McCaffrey, Nicola; Eckert, Danny J; McCloud, Philip; Louw, Sandra; Lam, Lawrence; Greene, Aine; Fazekas, Belinda; Clark, Katherine C; Fong, Kwun; Agar, Meera R; Joshi, Rohit; Kilbreath, Sharon; Ferreira, Diana; Ekström, Magnus

2017-01-01

Introduction Chronic breathlessness is highly prevalent and distressing to patients and families. No medication is registered for its symptomatic reduction. The strongest evidence is for regular, low-dose, extended- release (ER) oral morphine. A recent large phase III study suggests the subgroup most likely to benefit have chronic obstructive pulmonary disease (COPD) and modified Medical Research Council breathlessness scores of 3 or 4. This protocol is for an adequately powered, parallel-arm, placebo-controlled, multisite, factorial, block-randomised study evaluating regular ER morphine for chronic breathlessness in people with COPD. Methods and analysis The primary question is what effect regular ER morphine has on worst breathlessness, measured daily on a 0–10 numerical rating scale. Uniquely, the coprimary outcome will use a FitBit to measure habitual physical activity. Secondary questions include safety and, whether upward titration after initial benefit delivers greater net symptom reduction. Substudies include longitudinal driving simulation, sleep, caregiver, health economic and pharmacogenetic studies. Seventeen centres will recruit 171 participants from respiratory and palliative care. The study has five phases including three randomisation phases to increasing doses of ER morphine. All participants will receive placebo or active laxatives as appropriate. Appropriate statistical analysis of primary and secondary outcomes will be used. Ethics and dissemination Ethics approval has been obtained. Results of the study will be submitted for publication in peer-reviewed journals, findings presented at relevant conferences and potentially used to inform registration of ER morphine for chronic breathlessness. Trial registration number NCT02720822; Pre-results. PMID:28716797

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

Evaluation of Bacterial & Fungal Culture Practices in School Classrooms

ERIC Educational Resources Information Center

Weese, J. Scott

2009-01-01

A wide range of activities may be undertaken in elementary and secondary school science laboratories as part of regular curricular activities or optional classroom activities, including science fair projects. Among these is the culturing of microorganisms such as bacteria or fungi. There are various potential educational opportunities associated…

34 CFR 645.1 - What is the Upward Bound Program?

Code of Federal Regulations, 2010 CFR

2010-07-01

... participants the skills and motivation necessary to complete a program of secondary education and to enter and... the following three types of projects: (1) Regular Upward Bound projects. (2) Upward Bound Math and... Education Regulations of the Offices of the Department of Education (Continued) OFFICE OF POSTSECONDARY...

28 CFR 90.101 - What definitions apply for the grant program?

Code of Federal Regulations, 2010 CFR

2010-07-01

... program? 90.101 Section 90.101 Judicial Administration DEPARTMENT OF JUSTICE (CONTINUED) VIOLENCE AGAINST... education is defined to include an educational institution in any State that admits as regular students only... beyond secondary education; provides an educational program for which the institution has been granted...

A Program Based on Maslow's Hierarchy Helps Students in Trouble

ERIC Educational Resources Information Center

Yates, Mary Ruth; Saunders, Ron; Watkins, J. Foster

1980-01-01

The article discusses the development of an "alternative school" in an urban school system for students having trouble in the regular secondary setting. The program was based upon "Maslow's Hierarchy of Needs" and is described in detail. The initial assessment of the program produced very positive results.

Identity Development in Deaf Adolescents

ERIC Educational Resources Information Center

Kunnen, E. Saskia

2014-01-01

We studied identity development during 5 years in seven deaf adolescents who attended a school for deaf children in the highest level of regular secondary education (age between 14 and 18 years), administering identity interviews every year. Identity development is conceptualized as the processes of exploration and commitment formation (Bosma,…

Response to Intervention: The Future for Secondary Schools

ERIC Educational Resources Information Center

Canter, Andrea; Klotz, Mary Beth; Cowan, Katherine

2008-01-01

Response to intervention (RTI) program is a tiered process of implementing evidence-based instructional strategies in the regular education setting and frequently measuring the student's progress to determine whether these strategies are effective. The use of RTI methods as part of a comprehensive system to address student learning difficulties…

THE MARK TWAIN SUMMER INSTITUTE. 1964 ANNUAL REPORT.

ERIC Educational Resources Information Center

LEMEN, ROBERT F.; AND OTHERS

INTELLECTUALLY ABLE SECONDARY SCHOOL STUDENTS APPLIED FOR THE INSTITUTE. COURSES OFFERED WERE NOT FOR CREDIT BUT WERE SUPPLEMENTARY TO THE REGULAR CURRICULUM. A SMALL TUITION WAS PAID FOR THE ONE COURSE CHOSEN. THE COURSES OFFERED INCLUDED ENGLISH COMPOSITION AND LITERATURE, BEGINNING CHINESE, ADVANCED CHINESE, GERMAN, JAPANESE, BEGINNING RUSSIAN,…

Consistent Partial Least Squares Path Modeling via Regularization

PubMed Central

Jung, Sunho; Park, JaeHong

2018-01-01

Partial least squares (PLS) path modeling is a component-based structural equation modeling that has been adopted in social and psychological research due to its data-analytic capability and flexibility. A recent methodological advance is consistent PLS (PLSc), designed to produce consistent estimates of path coefficients in structural models involving common factors. In practice, however, PLSc may frequently encounter multicollinearity in part because it takes a strategy of estimating path coefficients based on consistent correlations among independent latent variables. PLSc has yet no remedy for this multicollinearity problem, which can cause loss of statistical power and accuracy in parameter estimation. Thus, a ridge type of regularization is incorporated into PLSc, creating a new technique called regularized PLSc. A comprehensive simulation study is conducted to evaluate the performance of regularized PLSc as compared to its non-regularized counterpart in terms of power and accuracy. The results show that our regularized PLSc is recommended for use when serious multicollinearity is present. PMID:29515491

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.

Quantitation of Oxidative Modifications of Commercial Human Albumin for Clinical Use.

PubMed

Takahashi, Teppei; Terada, Tomoyoshi; Arikawa, Hajime; Kizaki, Kazuha; Terawaki, Hiroyuki; Imai, Hajime; Itoh, Yoshinori; Era, Seiichi

2016-01-01

We investigated the quantitation of oxidative chemical modifications, such as thiol oxidation and carbonylation, in medical-grade human serum albumin (HSA) preparations, in comparison with those of healthy and diseased subjects. Four kinds of HSA products were obtained from three major suppliers in Japan. Eight male collegiate students and six healthy male volunteers were recruited as the young (21.6 years) and older (57.2 years) groups, respectively. Four male stable patients (64.3 years) treated with regular hemodialysis (HD) also enrolled in this study. Quantitative analyses for thiol oxidation and carbonylation were performed using HPLC and spectroscopic methods, respectively. Structural characterization was further investigated by differential scanning calorimetry (DSC) and circular dichroism (CD) spectropolarimetry. Significantly larger amounts of thiol-oxidized and carbonylated HSA products were observed than HSA obtained from healthy subjects. In the structural characterization, the midpoint temperature of the denaturation curve (Tm) analyzed by DSC was relatively high, and may have been caused by the added albumin-specific stabilizers, and CD-resolved secondary structure showed that HSA products had a helical conformation. Commercial HSA products for clinical use have a more thermally stable state and remain in a helix-rich structure, even though their specific amino acids (mainly Cys and Lys residues) are oxidatively modified.

Network structure exploration in networks with node attributes

NASA Astrophysics Data System (ADS)

Chen, Yi; Wang, Xiaolong; Bu, Junzhao; Tang, Buzhou; Xiang, Xin

2016-05-01

Complex networks provide a powerful way to represent complex systems and have been widely studied during the past several years. One of the most important tasks of network analysis is to detect structures (also called structural regularities) embedded in networks by determining group number and group partition. Most of network structure exploration models only consider network links. However, in real world networks, nodes may have attributes that are useful for network structure exploration. In this paper, we propose a novel Bayesian nonparametric (BNP) model to explore structural regularities in networks with node attributes, called Bayesian nonparametric attribute (BNPA) model. This model does not only take full advantage of both links between nodes and node attributes for group partition via shared hidden variables, but also determine group number automatically via the Bayesian nonparametric theory. Experiments conducted on a number of real and synthetic networks show that our BNPA model is able to automatically explore structural regularities in networks with node attributes and is competitive with other state-of-the-art models.

[Meals consumption among thirteen years olds and selected family socio-economic correlates].

PubMed

Korzycka-Stalmach, Magdalena; Mikiel-Kostyra, Krystyna; Oblacińska, Anna; Jodkowska, Maria; Wojdan-Godek, Elzbieta

2010-01-01

To analyse the influence of selected family socioeconomic factors on the regularity of meals consumption among 13-years aged adolescents. Group of 605 13-years olds identified in the prospective cohort study in 2008 was analysed. Data was gathered with use of posted questionnaires. On the basis of information given by children the regularity (4-5 times a week) of meals consumption on school days and eating meals with parents were correlated with parents' educational level, occupational status and perceived family wealth. The study also recognised the distinction between urban and rural residents. Most questionnaires were filled out by mothers (95%), only 5% by fathers. In urban area, the mother's occupation and the perceived family wealth, correlate with children meals consumption and eating meals with parents. Children whose mothers have a job eat breakfast 1.5 times and supper 3 times less regularly, than children whose mothers don't work. Children from poor families eat breakfast 14 times less regularly than children from rich families as well as eat supper 3 times less regularly than children from average wealthy families. In the rural area, the regularity of meals consumption significantly influence the mother's education. Children whose mothers have a secondary education, compared with children of mothers with basic education, are 4 times more likely to eat dinner and supper regularly. The family socioeconomic factors significantly correlate with regularity of 13-years olds meals consumption and regularity of family meals. The place of residence involve the different factors influencing meals consumption habits. It was shown that children and fathers were too little engaged in family life, including family meals preparation and consumption.

On the regularized fermionic projector of the vacuum

NASA Astrophysics Data System (ADS)

Finster, Felix

2008-03-01

We construct families of fermionic projectors with spherically symmetric regularization, which satisfy the condition of a distributional MP-product. The method is to analyze regularization tails with a power law or logarithmic scaling in composite expressions in the fermionic projector. The resulting regularizations break the Lorentz symmetry and give rise to a multilayer structure of the fermionic projector near the light cone. Furthermore, we construct regularizations which go beyond the distributional MP-product in that they yield additional distributional contributions supported at the origin. The remaining freedom for the regularization parameters and the consequences for the normalization of the fermionic states are discussed.

Traveling in the dark: the legibility of a regular and predictable structure of the environment extends beyond its borders.

PubMed

Yaski, Osnat; Portugali, Juval; Eilam, David

2012-04-01

The physical structure of the surrounding environment shapes the paths of progression, which in turn reflect the structure of the environment and the way that it shapes behavior. A regular and coherent physical structure results in paths that extend over the entire environment. In contrast, irregular structure results in traveling over a confined sector of the area. In this study, rats were tested in a dark arena in which half the area contained eight objects in a regular grid layout, and the other half contained eight objects in an irregular layout. In subsequent trials, a salient landmark was placed first within the irregular half, and then within the grid. We hypothesized that rats would favor travel in the area with regular order, but found that activity in the area with irregular object layout did not differ from activity in the area with grid layout, even when the irregular half included a salient landmark. Thus, the grid impact in one arena half extended to the other half and overshadowed the presumed impact of the salient landmark. This could be explained by mechanisms that control spatial behavior, such as grid cells and odometry. However, when objects were spaced irregularly over the entire arena, the salient landmark became dominant and the paths converged upon it, especially from objects with direct access to the salient landmark. Altogether, three environmental properties: (i) regular and predictable structure; (ii) salience of landmarks; and (iii) accessibility, hierarchically shape the paths of progression in a dark environment. Copyright © 2012 Elsevier B.V. All rights reserved.

A theoretical prediction of the paradoxical surface free energy for FCC metallic nanosolids

NASA Astrophysics Data System (ADS)

Abdul-Hafidh, Esam H.; Aïssa, Brahim

2016-08-01

We report on the development of an efficient and simple method to calculate the surface free energy (surface tension) of a general-shaped metallic nanosolid. Both nanoparticles and nanostructures that account for the crystal structure and size were considered. The surface free energy of a face-centered cubic structure of a metallic nanoparticles was found to decrease as the size decreases, for a shape factor equal to 1.0 (i.e., spherical). However, when the shape factor exceeds this value, which includes disk-like, regular tetrahedral, regular hexahedral, regular octahedral, nanorod, and regular quadrangular structures, the behavior of the surface free energy was found to reverse, especially for small nanoparticles and then increases as the size decreases. Moreover, this behavior was systematically recorded for large nanoparticles when the mechanical distortion was appreciable. As a matter of fact, this model was also applied to the noble transition metals, including gold and silver nanoparticles. This work is a clear step forward establishing a systematic mechanism for controlling the mechanical properties of nanoscale particles by controlling the shape, size and structure.

Multistep modeling (MSM) of biomolecular structure application to the A-G mispair in the B-DNA environment

NASA Technical Reports Server (NTRS)

Srinivasan, S.; Raghunathan, G.; Shibata, M.; Rein, R.

1986-01-01

A multistep modeling procedure has been evolved to study the structural changes introduced by lesions in DNA. We report here the change in the structure of regular B-DNA geometry due to the incorporation of Ganti-Aanti mispair in place of a regular G-C pair, preserving the helix continuity. The energetics of the structure so obtained is compared with the Ganti-Asyn configuration under similar constrained conditions. We present the methodology adopted and discuss the results.

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.

The value of multidisciplinary team meetings within an early pregnancy assessment unit.

PubMed

Bharathan, Rasiah; Farag, Mena; Hayes, Kevin

2016-08-01

This is the first study to ascertain the value of multidisciplinary team (MDT) meetings within an early pregnancy assessment unit (EPAU). Our national telephone survey identified that in the United Kingdom, overall 37% of EPAU utilise regular MDT meetings. Secondary and tertiary hospitals are just as likely to hold regular MDT meetings. The participants in our interview study expressed the principal benefits of regular MDT meetings as communication, education and effective stress management. The perceived additional benefits included improved care quality, better patient experience and enhanced team cohesion. During the meetings, at least, one representative from every tier of staffing was present. The caseload of the MDT meeting comprised ectopic pregnancies and pregnancies of unknown location. We propose a number of research studies, which would build on this study. Such efforts will help enhance the effectiveness of the MDT-based EPAU service.

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.

Intermixed adatom and surface-bound adsorbates in regular self-assembled monolayers of racemic 2-butanethiol on Au(111).

PubMed

Ouyang, Runhai; Yan, Jiawei; Jensen, Palle S; Ascic, Erhad; Gan, Shiyu; Tanner, David; Mao, Bingwei; Niu, Li; Zhang, Jingdong; Tang, Chunguang; Hush, Noel S; Reimers, Jeffrey R; Ulstrup, Jens

2015-04-07

In situ scanning tunneling microscopy combined with density functional theory molecular dynamics simulations reveal a complex structure for the self-assembled monolayer (SAM) of racemic 2-butanethiol on Au(111) in aqueous solution. Six adsorbate molecules occupy a (10×√3)R30° cell organized as two RSAuSR adatom-bound motifs plus two RS species bound directly to face-centered-cubic and hexagonally close-packed sites. This is the first time that these competing head-group arrangements have been observed in the same ordered SAM. Such unusual packing is favored as it facilitates SAMs with anomalously high coverage (30%), much larger than that for enantiomerically resolved 2-butanethiol or secondary-branched butanethiol (25%) and near that for linear-chain 1-butanethiol (33%). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High-resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer.

PubMed Central

Abele, U.; Schulz, G. E.

1995-01-01

The structure of adenylate kinase from yeast ligated with the two-substrate-mimicking inhibitor Ap5A and Mg2+ has been refined to 1.96 A resolution. In addition, the refined structure of the same complex with a bound imidazole molecule replacing Mg2+ has been determined at 1.63 A. These structures indicate that replacing Mg2+ by imidazole disturbs the water structure and thus the complex. A comparison with the G-proteins shows that Mg2+ is exactly at the same position with respect to the phosphates. However, although the Mg2+ ligand sphere of the G-proteins is a regular octahedron containing peptide ligands, the reported adenylate kinase has no such ligands and an open octahedron leaving space for the Mg2+ to accompany the transferred phosphoryl group. A superposition of the known crystalline and therefore perturbed phosphoryl transfer geometries in the adenylate kinases demonstrates that all of them are close to the start of the forward reaction with bound ATP and AMP. Averaging all observed perturbed structures gives rise to a close approximation of the transition state, indicating in general how to establish an elusive transition state geometry. The average shows that the in-line phosphoryl transfer is associative, because there is no space for a dissociative metaphosphate intermediate. As a side result, the secondary dipole interaction in the alpha-helices of both protein structures has been quantified. PMID:7670369

A Study of Instructional Methods Used in Fast-Paced Classes

ERIC Educational Resources Information Center

Lee, Seon-Young; Olszewski-Kubilius, Paula

2006-01-01

This study involved 15 secondary-level teachers who taught fast-paced classes at a university based summer program and similar regularly paced classes in their local schools in order to examine how teachers differentiate or modify instructional methods and content selections for fast-paced classes. Interviews were conducted with the teachers…

34 CFR 600.5 - Proprietary institution of higher education.

Code of Federal Regulations, 2010 CFR

2010-07-01

... institution of higher education is an educational institution that— (1) Is not a public or private nonprofit educational institution; (2) Is in a State; (3) Admits as regular students only persons who— (i) Have a high... legally authorized to provide an educational program beyond secondary education in the State in which the...

The Effects of Chiropractic Treatment on Students With Learning and Behavioral Impairments Due to Neurological Dysfunction.

ERIC Educational Resources Information Center

Walton, E. V.; Brzozowski, Walter T.

The effects of chiropractic treatment on children with learning and behavioral problems was investigated with 24 elementary and secondary level students, 12 receiving regular chiropractic treatment and 12 receiving medication. Results indicated that chiropractic treatment was more effective for the wide range symptoms common in the neurological…

Developing a Professional Learning Community among Preservice Teachers

ERIC Educational Resources Information Center

Bond, Nathan

2013-01-01

This action research study examined the development of a professional learning community (PLC) among 20 preservice secondary teachers as they met regularly during a semester-long, field-based education course to share artifacts of learning from their professional portfolios. The PLC model described by Hord and Tobia (2012) served as a framework…

The Elementary School Guidance Counselor: A Developmental Model.

ERIC Educational Resources Information Center

Gum, Moy F.

The position taken is that elementary schools need a guidance program and an elementary school guidance counselor who is a regular member of a given school staff. However, it is advocated that elementary guidance should not be merely an extension of the secondary guidance program. The viewpoint taken here is that elementary guidance should be…

Does the Modality Principle for Multimedia Learning Apply to Science Classrooms?

ERIC Educational Resources Information Center

Harskamp, Egbert G.; Mayer, Richard E.; Suhre, Cor

2007-01-01

This study demonstrated that the modality principle applies to multimedia learning of regular science lessons in school settings. In the first field experiment, 27 Dutch secondary school students (age 16-17) received a self-paced, web-based multimedia lesson in biology. Students who received lessons containing illustrations and narration performed…

Assessment of Metacognitive Knowledge in Students with Special Educational Needs

ERIC Educational Resources Information Center

Händel, Marion; Lockl, Kathrin; Heydrich, Jana; Weinert, Sabine; Artelt, Cordula

2014-01-01

This study investigated whether and, if so, how metacognitive knowledge can be assessed validly in students with special educational needs in a large-scale assessment like the German National Educational Panel Study. In total, 804 sixth-grade students including both regular school students attending the lowest track of secondary education…

Principal Succession and Its Impact on Teacher Morale

ERIC Educational Resources Information Center

Meyer, Matthew J.; Macmillan, Robert B.; Northfield, Shawn

2009-01-01

Our detailed study of two secondary schools in Nova Scotia which had experienced regular principal succession examined succession and its impact on teacher morale. We found that the process of principal succession and the new principal's practices have the potential to change a school culture and both positively and negatively affect teacher and…

Teaching Rhetoric Today: Ancient Exercises for Contemporary Citizens

ERIC Educational Resources Information Center

Dainville, Julie; Sans, Benoît

2016-01-01

Since July 2013, our research team has been working on a project that aims at re-introducing rhetorical exercises in Belgian secondary (high) schools and at studying their effects on the pupils. Our hypothesis is that the regular practice of rhetorical exercises, inspired by those practised in Antiquity, could stimulate skills like…

The Relative Effects of University Success Courses and Individualized Interventions for Students with Learning Disabilities

ERIC Educational Resources Information Center

Reed, Maureen J.; Kennett, Deborah J.; Lewis, Tanya; Lund-Lucas, Eunice; Stallberg, Carolyn; Newbold, Inez L.

2009-01-01

Little is known about the relative effects of post-secondary learning services for students with learning disabilities. We compared outcomes for students with learning disabilities who selected to: (1) take an academic learning success course (course-intervention), (2) have regular individual interventions (high-intervention) or (3) use services…

34 CFR 643.21 - What selection criteria does the Secretary use?

Code of Federal Regulations, 2011 CFR

2011-07-01

... following— (i) Low-income families residing in the target area; or (ii) Students attending the target... among individuals in the target schools as evidenced by the annual student persistence rates in the... students in the target school or schools who graduate high school with a regular secondary school diploma...

English as a Second Language/Dialect Resource Book for K-12.

ERIC Educational Resources Information Center

British Columbia Dept. of Education, Victoria. Curriculum Development Branch.

This resource guide is designed for use by all educators who work with English-as-a-Second-Language/Dialect (ESL/D) students, including administrators, regular classroom teachers in both elementary and secondary schools, trained ESL/D teachers, and other support staff such as language assistance teachers and special education staff. The book…

Examining Predictors of Breakfast Skipping and Breakfast Program Use among Secondary School Students in the Compass Study

ERIC Educational Resources Information Center

Godin, Katelyn M.; Patte, Karen A.; Leatherdale, Scott T.

2018-01-01

Background: Many Canadian schools offer breakfast programs; however, students' engagement in these programs is low, while breakfast skipping is highly prevalent among youth. This study examined whether the availability of breakfast programs supports adolescents' regular breakfast eating, and identified characteristics of breakfast skippers who are…

42 CFR 411.162 - Medicare benefits secondary to group health plan benefits.

Code of Federal Regulations, 2012 CFR

2012-10-01

... course of maintenance dialysis or who receive a kidney transplant before December 1989, the coordination... entitlement. (3) An individual began a regular course of maintenance dialysis on February 10, 1990. He did not... plan coverage and Medicare made no payments at all during the deferred period.) (8) The same facts...

42 CFR 411.162 - Medicare benefits secondary to group health plan benefits.

Code of Federal Regulations, 2011 CFR

2011-10-01

... course of maintenance dialysis or who receive a kidney transplant before December 1989, the coordination... entitlement. (3) An individual began a regular course of maintenance dialysis on February 10, 1990. He did not... plan coverage and Medicare made no payments at all during the deferred period.) (8) The same facts...

42 CFR 411.162 - Medicare benefits secondary to group health plan benefits.

Code of Federal Regulations, 2014 CFR

2014-10-01

... course of maintenance dialysis or who receive a kidney transplant before December 1989, the coordination... entitlement. (3) An individual began a regular course of maintenance dialysis on February 10, 1990. He did not... plan coverage and Medicare made no payments at all during the deferred period.) (8) The same facts...

Depictions of Human Bodies in the Illustrations of Early Childhood Textbooks

ERIC Educational Resources Information Center

Martínez-Bello, Vladimir E.; Martínez-Bello, Daniel A.

2016-01-01

In many Ibero-American countries children in the early childhood education (ECE) system have the opportunity to interact with textbooks on a regular basis. The powerful social function of textbooks in socializing children in primary and secondary school, and in legitimizing what counts as cultural norms and officially sanctioned values and…

Teaching Handicapped Students English: A Resource Handbook for K-12 Teachers.

ERIC Educational Resources Information Center

Price, Jane W., Ed.

One of five volumes devoted to teaching content subjects to the handicapped, the book addresses ways in which elementary and secondary regular class teachers have successfully worked with mainstreamed students in English. The following titles and authors are included: "Chris Learns to Read" (E. Roake); "Working Together" (B. Bodner-Johnson);…

Orchestra Festival Evaluations: Interjudge Agreement and Relationships between Performance Categories and Final Ratings.

ERIC Educational Resources Information Center

Garman, Barry R.; And Others

1991-01-01

Band, orchestra, and choir festival evaluations are a regular part of many secondary school music programs, and most such festivals engage adjudicators who rate each group's performance. Because music ensemble performance is complex and multi-dimensional, it does not lend itself readily to precise measurement; generally, musical performances are…

The Law of Student Expulsions and Suspensions. Second Edition. Monograph Series, No. 62.

ERIC Educational Resources Information Center

Rossow, Lawrence F.; Parkinson, Jerry R.

In 1975, the Supreme Court decision in "Goss versus Lopez" established the foundation of procedural law in student suspensions. This text focuses on procedural aspects of the expulsion and suspension of students. It is devoted to the elementary and secondary public-school settings involving regular-education students. It describes how…

Growth Mindset of Gifted Seventh Grade Students in Science

ERIC Educational Resources Information Center

Esparza, Julie; Shumow, Lee; Schmidt, Jennifer A.

2014-01-01

Through secondary analysis of data collected in middle school science classrooms, this study (a) compared gifted and regular students' beliefs about the malleability of intelligence in science; (b) investigated whether teaching gifted and talented middle-school students about malleability of the brain and study skills helped them to develop a…

The Classical Heritage in America: A Curriculum Resource. Tentative Edition.

ERIC Educational Resources Information Center

Philadelphia School District, PA. Office of Curriculum and Instruction.

This curriculum resource is intended to help make students of Latin, Greek and other subjects more aware of America's classical heritage. It is designed to be used selectively by teachers to enrich the regular curriculum in classical languages in elementary and secondary schools. In providing background information for the teacher and suggestions…

Consumer Mathematics. Teacher's Guide [and Student Guide]. Parallel Alternative Strategies for Students (PASS).

ERIC Educational Resources Information Center

Walford, Sylvia B.; Thomas, Portia R.

This teacher's guide and student guide are designed to accompany a consumer mathematics textbook that contains supplemental readings, activities, and methods adapted for secondary students who have disabilities and other students with diverse learning needs. The materials are designed to help these students succeed in regular education content…

Transitions from High School--SPED Students. Research Brief

ERIC Educational Resources Information Center

Walker, Karen

2007-01-01

Helping regular education students transition from high school to the post-secondary world can be a daunting task. Assisting students with special needs do this can be quite intimidating. According to the Harris Poll 2000, 20% of the general population was unemployed, while 71% of adults with disabilities were unemployed (Miller, Lombard, &…

Tillamook's Learning Disabilities Program for Secondary Students. OSSC Bulletin, Vol. 24, No. 5.

ERIC Educational Resources Information Center

Johnson, Maggie

The Tillamook program provides support to learning disabled students who experience difficulty in science, social studies, and other content areas in the regular class setting, as a result of mainstreaming efforts. The program model includes a professionally staffed resource room, a diagnostic-prescriptive team, and a library of multimedia…

A Model Program of Comprehensive Educational Services for Students With Learning Problems.

ERIC Educational Resources Information Center

Union Township Board of Education, NJ.

Programs are described for learning-disabled or mantally-handicapped elementary and secondary students in regular and special classes in Union, New Jersey, and approximately 58 instructional episodes involving student made objects for understanding technology are presented. In part one, components of the model program such as the multi-learning…

Setting the Stage for Physical Activity for Secondary Students

ERIC Educational Resources Information Center

Ciccomascolo, Lori; Riebe, Deborah

2006-01-01

Despite the positive long-term physiological and psychological effects of exercise, many young adults between the ages of 12 and 21 years do not participate in regular physical activity. With the time constraints and other challenges in teaching and assessing students, physical educators need realistic strategies that will help in their efforts to…

Physical Science. Teacher's Guide [and Student Guide]. Parallel Alternative Strategies for Students (PASS).

ERIC Educational Resources Information Center

Danner, Greg, Ed.; Fresen, Sue, Ed.

This teacher's guide and student guide unit contains supplemental readings, activities, and methods adapted for secondary students who have disabilities and other students with diverse learning needs. The materials are designed to help these students succeed in regular education content courses and include simplified text and smaller units of…

Using Self-Recording, Evaluation, and Graphing to Increase Completion of Homework Assignments.

ERIC Educational Resources Information Center

Trammel, Diana Lynn; And Others

1994-01-01

Self-monitoring procedures were effective in increasing the number of daily homework assignments completed by eight secondary level students with learning disabilities. A daily listing of all assignments given by regular classroom teachers was used. Goal setting and self-graphing of data appeared to increase self-monitoring effectiveness. (DB)

Evaluation of Title I ESEA Projects: 1975-76.

ERIC Educational Resources Information Center

Philadelphia School District, PA. Office of Research and Evaluation.

Evaluation services to be provided during 1975-76 to projects funded under the Elementary and Secondary Education Act Title I are listed in this annual booklet. For each project, the following information is provided: goals to be assessed, evaluation techniques (design), and evaluation milestones. Regular term and summer term projects reported on…

Control of secondary instability of the crossflow and Görtler-like vortices (Success and problems)

NASA Astrophysics Data System (ADS)

Kozlov, Viktor V.; Grek, Genrich R.

The secondary instability on a group of crossflow vortices developing in a swept wing boundary layer is described. It is shown that, for travelling waves, there is a region of linear development, and the growth rate of disturbances appreciably depends on the separation between the vortices. Methods of controlling the secondary instability of the vortices by a controlled wave and local suction are proposed and substantiated. The stability of a flat plate boundary layer modulated by G&ou ml;rtler-like stationary vortices is described. Vortices were generated inside the boundary layer by means of roughness elements arranged in a regular array along the spanwise (z) direction. Transition is not caused directly by these structures, but by the growth of small amplitude travelling waves riding on top of the steady vortices. This situation is analogous to the transition process in Görtler and cross-flows. The waves were found to amplify up to a stage where higher harmonics are gener ated, leading to turbulent breakdown and disintegration of the spanwise boundary layer structure. For strong modulations, the observed instability is quite powerful, and can be excited "naturally" by small uncontrollable background disturbances. Controlled oscillations were then introduced by means of a vibrating ribbon, allowing a detailed investigation of the wave characteristics. The instability seems to be associated with the spanwise gradients of the mean flow, , and at all z-positions, the maximum wave amplitude was found at a wall-normal position where the mean velocity is equal to the phase velocity of the wave, U(y)=c, i.e., at the local critical layer. Unstable waves were observed at frequency well above those for which Tollmien-Schlichting (TS) waves amplify in the Blasius boundary layer. Excitation at lower frequencies and milder basic flow modulation showed that TS-type waves may a lso develop. Study of the transition control in that flow by means of riblets shows that the effect of the riblets is to suppress longitudinal vortex structures in a boundary layer. The boundary layer becomes stable with respect to high-frequency travelling waves, which cause the transition in the absence of the riblets.

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

The Evolution of Frequency Distributions: Relating Regularization to Inductive Biases through Iterated Learning

ERIC Educational Resources Information Center

Reali, Florencia; Griffiths, Thomas L.

2009-01-01

The regularization of linguistic structures by learners has played a key role in arguments for strong innate constraints on language acquisition, and has important implications for language evolution. However, relating the inductive biases of learners to regularization behavior in laboratory tasks can be challenging without a formal model. In this…

[Alcohol use in young adolescents. A survey in French secondary schools].

PubMed

Bailly, D; Rouchaud, A; Garcia, C; Roehrig, C; Ferley, J-P

2015-05-01

Among young adolescents, early use of alcohol has been shown to be related to later alcohol use disorders and alcohol-related problems in numerous epidemiologic studies. However, if drinking problems are now well documented in young people, few data are available on alcohol use in children and young adolescents. The purpose of this study was to examine the perceptions and attitudes with respect to alcohol use among young adolescents entering their first year of secondary school (mean age, 11.5 years). Data were collected from the ESPACE program, a preventive program conducted in the educational district of Limoges, France. Of the 2268 respondents with complete data, 73.4% (77.1% in males vs. 69.9% in females; P<0.001) reported having tasted alcohol drinks and 3.7% (4.9% in males vs. 2.6% in females; P=0.004) having experienced drunkenness at least once. Of these adolescents, 5.4% (8.5% in males vs. 2.4% in females, P<0.001) reported consuming alcohol at least once per month, which may be considered as a sort of regular drinking pattern. Taking age, sex, and level of alcohol consumption into account, experience of drunkenness (21.9% in regular users vs. 3.7% in occasional users), tobacco use (25.8% in regular users vs. 12.6% in occasional users and 1.5% in nonusers) and cannabis use (6.0% in regular users vs. 0.9% in occasional users and 0.2% in nonusers) were found to be significantly more frequent in regular alcohol users than in other students (P<0.001). Data analysis also showed that regular alcohol users felt significantly more frequently depressed, lacking self-assurance, dissatisfied with their physical appearance and their way of life, and they felt that they exhibited significantly more impairments in their interactions with parents, peers, and the school environment. Similarly, they were found to have significantly more frequently an inclination for risk behaviors and a significantly more positive view of drinking than other students. These results look almost like those reported in adolescents and young people, and show that the alcohol abuse pattern is drawn early in childhood. They also highlight the value of epidemiologic investigations for planning preventive interventions. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

School Soft Drink Availability and Consumption Among U.S. Secondary Students

PubMed Central

Terry-McElrath, Yvonne M.; O’Malley, Patrick M.; Johnston, Lloyd D.

2013-01-01

Background Consumption of sugar-sweetened beverages (SSBs) such as soft drinks has been associated with significantly increased energy intake and body weight. One strategy used to reduce soft drink consumption among adolescents has been reducing availability in schools; however, research is limited on associations between availability of soft drinks in school and student consumption. Purpose This study examines associations between regular and diet soft drink availability in schools and student consumption using data from 329 secondary schools and 9284 students. Methods Data were obtained from two sources: (1) nationally representative cross-sectional samples of students in Grades 8, 10, and 12 from U.S. public and private schools in 2010 and 2011 in the Monitoring the Future study; and (2) administrators of the same schools in the Youth, Education, and Society study. Multilevel modeling conducted in 2012 examined associations between school availability and student consumption controlling for student sociodemographics and school characteristics. Results In the total sample of more than 9000 students, regular and diet soft drink availability in school was not related to student consumption of these beverages in multivariate models. Yet, among African-American high school students, school regular and diet soft drink availability was significantly related to higher daily consumption (both before and after controlling for student and school factors). Conclusions Although removal of soft drinks from schools may not result in significantly lower overall student consumption, such actions may result in significant decreases in soft drink consumption for specific student groups. PMID:23683974

Ideal regularization for learning kernels from labels.

PubMed

Pan, Binbin; Lai, Jianhuang; Shen, Lixin

2014-08-01

In this paper, we propose a new form of regularization that is able to utilize the label information of a data set for learning kernels. The proposed regularization, referred to as ideal regularization, is a linear function of the kernel matrix to be learned. The ideal regularization allows us to develop efficient algorithms to exploit labels. Three applications of the ideal regularization are considered. Firstly, we use the ideal regularization to incorporate the labels into a standard kernel, making the resulting kernel more appropriate for learning tasks. Next, we employ the ideal regularization to learn a data-dependent kernel matrix from an initial kernel matrix (which contains prior similarity information, geometric structures, and labels of the data). Finally, we incorporate the ideal regularization to some state-of-the-art kernel learning problems. With this regularization, these learning problems can be formulated as simpler ones which permit more efficient solvers. Empirical results show that the ideal regularization exploits the labels effectively and efficiently. Copyright © 2014 Elsevier Ltd. All rights reserved.

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.

A multiplicative regularization for force reconstruction

NASA Astrophysics Data System (ADS)

Aucejo, M.; De Smet, O.

2017-02-01

Additive regularizations, such as Tikhonov-like approaches, are certainly the most popular methods for reconstructing forces acting on a structure. These approaches require, however, the knowledge of a regularization parameter, that can be numerically computed using specific procedures. Unfortunately, these procedures are generally computationally intensive. For this particular reason, it could be of primary interest to propose a method able to proceed without defining any regularization parameter beforehand. In this paper, a multiplicative regularization is introduced for this purpose. By construction, the regularized solution has to be calculated in an iterative manner. In doing so, the amount of regularization is automatically adjusted throughout the resolution process. Validations using synthetic and experimental data highlight the ability of the proposed approach in providing consistent reconstructions.

An assessment of secondary traumatic stress in juvenile justice education workers.

PubMed

Smith Hatcher, Schnavia; Bride, Brian E; Oh, Hyejung; Moultrie King, Dione; Franklin Catrett, James

2011-07-01

Given the frequency and violent character of the traumas encountered by juvenile offenders, staff members who regularly interact with juveniles in custody are at risk of developing secondary traumatic stress. Juvenile justice teachers and staff (N = 118) were administered a cross-sectional survey, including the Secondary Traumatic Stress Scale. Respondents said the students were moderately traumatized (47%), severely traumatized (27%), and very severely traumatized (7%). Regarding STS, the most frequently reported symptom was intrusive thoughts related to work with the students, mentioned by 61% of respondents. Additionally, 81% met at least one, 55% met two, and 39% met all three core diagnostic criteria for posttraumatic stress disorder. Recommendations for juvenile justice staff members and for the organization are provided to address practice and policy implications.

An Assessment of Secondary Traumatic Stress in Juvenile Justice Education Workers

PubMed Central

Hatcher, Schnavia Smith; Bride, Brian E.; Oh, Hyejung; King, Dione Moultrie; Catrett, James “Jack” Franklin

2013-01-01

Given the frequency and violent character of the traumas encountered by juvenile offenders, staff members who regularly interact with juveniles in custody are at risk of developing secondary traumatic stress. Juvenile justice teachers and staff (N = 118) were administered a cross-sectional survey, including the Secondary Traumatic Stress Scale. Respondents said the students were moderately traumatized (47%), severely traumatized (27%), and very severely traumatized (7%). Regarding STS, the most frequently reported symptom was intrusive thoughts related to work with the students, mentioned by 61% of respondents. Additionally, 81% met at least one, 55% met two, and 39% met all three core diagnostic criteria for posttraumatic stress disorder. Recommendations for juvenile justice staff members and for the organization are provided to address practice and policy implications. PMID:21571748

Physician's practices and perspectives regarding tobacco cessation in a teaching hospital in Mysore City, Karnataka.

PubMed

Saud, Mohammed; Madhu, B; Srinath, K M; Ashok, N C; Renuka, M

2014-01-01

Tobacco is a leading cause of disease and premature death. Most of the smokers visit a doctor for various health related ailments and thus such clinic visits provide many opportunities for interventions and professional tobacco cessation advice. The primary aim of the following study is to assess the physician practices, perspectives, resources, barriers and education relating to tobacco cessation and their perceived need for training for the same. The secondary aim is to compare the physician's cessation practices from patient's perspective. A descriptive study was conducted in a hospital attached to Medical College in Mysore city, Karnataka. Information about doctor's practices, perspectives and their perceived need for training in tobacco cessation were collected using pre-structured self-administered Questionnaire, which were distributed in person. Patient's practices and perspectives were assessed using a pre-structured Oral Questionnaire. Almost 95% of physicians said that they ask patients about their smoking status and 94% advise them to quit smoking, but only 50% assist the patient to quit smoking and only 28% arrange follow-up visits. Thus, they do not regularly provide assistance to help patients quit, even though 98% of the physicians believed that helping patients to quit was a part of their role. Only 18% and 35% of the physicians said that Undergraduate Medical Education and Post Graduate Medical Education respectively prepared them very well to participate in smoking cessation activities. Tobacco cessation requires repeated and regular assistance. Such assistance is not being provided to patients by attending doctors. Our medical education system is failing to impart the necessary skills to doctors, needed to help patients quit smoking. Reforms in education are needed so as to prepare the physician to effectively address this problem.

Restrictions of physical activity participation in older adults with disability: employing keyword network analysis.

PubMed

Koo, Kyo-Man; Kim, Chun-Jong; Park, Chae-Hee; Byeun, Jung-Kyun; Seo, Geon-Woo

2016-08-01

Older adults with disability might have been increasing due to the rapid aging of society. Many studies showed that physical activity is an essential part for improving quality of life in later lives. Regular physical activity is an efficient means that has roles of primary prevention and secondary prevention. However, there were few studies regarding older adults with disability and physical activity participation. The purpose of this current study was to investigate restriction factors to regularly participate older adults with disability in physical activity by employing keyword network analysis. Two hundred twenty-nine older adults with disability who were over 65 including aging with disability and disability with aging in type of physical disability and brain lesions defined by disabled person welfare law partook in the open questionnaire assessing barriers to participate in physical activity. The results showed that the keyword the most often used was 'Traffic' which was total of 21 times (3.47%) and the same proportion as in the 'personal' and 'economical'. Exercise was considered the most central keyword for participating in physical activity and keywords such as facility, physical activity, disabled, program, transportation, gym, discomfort, opportunity, and leisure activity were associated with exercise. In conclusion, it is necessary to educate older persons with disability about a true meaning of physical activity and providing more physical activity opportunities and decreasing inconvenience should be systematically structured in Korea.

[An exploratory study of 'blended' cognitive behavioural therapy (CBT) for patients with a panic disorder: results and patients' experiences].

PubMed

Bruinsma, A; Kampman, M; Exterkate, C C; Hendriks, G J

2016-01-01

Digital technology (e-health or 'blended' care), combined with evidence-based face-to-face CBT, is becoming increasingly implemented into mental health care and is expected to result in improved effectiveness and efficiency. To explore the feasibility of blended CBT for patients with a panic disorder. Nine face-to-face sessions of blended CBT (n = 18), supplemented with the digital support of a tabletcomputer and three e-mail contacts, were compared with 12 weekly sessions of regular CBT (n = 18). Primary outcomes were panic frequency and avoidance behaviour; the secondary outcome was general functioning. Patients' experiences of the treatment were collected in the form of a structured interview. The effect sizes found in both the regular and the blended CBT were medium to high (Cohen's d 0.42-1.60). In both types of treatment there was a significant reduction in patients' symptoms. There were no big differences in patient satisfaction regarding the treatment received. The therapists registered 39 face-to-face minutes in the blended treatment but they registered in total 41 fewer face-to-face minutes; this represented a time reduction of 4%. Blended CBT with help of a tablet computer seems to be a suitable method for treating panic disorder psychologically, although the time saved is only moderate. Much more research is needed to ascertain the feasibility and the cost effectiveness of blended CBT.

Brisk walking can promote functional recovery in chronic stroke patients.

PubMed

Batcho, Charles Sèbiyo; Stoquart, Gaëtan; Thonnard, Jean-Louis

2013-09-01

To determine whether regular brisk walking can promote functional recovery in community-dwelling stroke patients. A total of 44 chronic stroke patients, recruited in Belgium and Benin, respectively European high-income and African low-income countries. This longitudinal, single-cohort, observational study with 1 intervention period and 4 time-points of assessments (2 baseline, 1 post-intervention and 1 follow-up) was structured in 3 periods: pre-intervention period (1 month), intervention period (3 months) and follow-up period (3 month). Intervention consisted of a 3 times/week group-based brisk walking programme. Primary outcome measures were ACTIVLIM-Stroke questionnaire and the 6-minute walk test (6MWT). Secondary outcome measures were the Stroke Impairment Assessment Set (SIAS), the Hospital Anxiety and Depression Scale (HADS), and the Berg Balance Scale (BBS). All outcome measures were stable during the pre-intervention period (p ≥ 0.16). They all improved significantly after intervention (p ≤ 0.01), except the HADS (p = 0.058). However, during the follow-up period, SIAS (p = 0.002) and BBS (p = 0.001) decreased, while ACTIVLIM-Stroke, 6MWT and HADS showed no significant change (p ≥ 0.13). This study suggests regular brisk walking as an effective approach to promote functional recovery in chronic stroke survivors. However, further studies are required before generalizing these results to the whole stroke population.

Seeking Temporal Predictability in Speech: Comparing Statistical Approaches on 18 World Languages.

PubMed

Jadoul, Yannick; Ravignani, Andrea; Thompson, Bill; Filippi, Piera; de Boer, Bart

2016-01-01

Temporal regularities in speech, such as interdependencies in the timing of speech events, are thought to scaffold early acquisition of the building blocks in speech. By providing on-line clues to the location and duration of upcoming syllables, temporal structure may aid segmentation and clustering of continuous speech into separable units. This hypothesis tacitly assumes that learners exploit predictability in the temporal structure of speech. Existing measures of speech timing tend to focus on first-order regularities among adjacent units, and are overly sensitive to idiosyncrasies in the data they describe. Here, we compare several statistical methods on a sample of 18 languages, testing whether syllable occurrence is predictable over time. Rather than looking for differences between languages, we aim to find across languages (using clearly defined acoustic, rather than orthographic, measures), temporal predictability in the speech signal which could be exploited by a language learner. First, we analyse distributional regularities using two novel techniques: a Bayesian ideal learner analysis, and a simple distributional measure. Second, we model higher-order temporal structure-regularities arising in an ordered series of syllable timings-testing the hypothesis that non-adjacent temporal structures may explain the gap between subjectively-perceived temporal regularities, and the absence of universally-accepted lower-order objective measures. Together, our analyses provide limited evidence for predictability at different time scales, though higher-order predictability is difficult to reliably infer. We conclude that temporal predictability in speech may well arise from a combination of individually weak perceptual cues at multiple structural levels, but is challenging to pinpoint.

Interaction of a digestive protease, Candida rugosa lipase, with three surfactants investigated by spectroscopy, molecular docking and enzyme activity assay.

PubMed

Zhang, Rui; Liu, Yang; Huang, Xinran; Xu, Mengchen; Liu, Rutao; Zong, Wansong

2018-05-01

The extensive use of surfactants in food, laundry products and agriculture has caused concern about their biosafety. However, few studies have been done on their potential effect on the lipase which has always been used with surfactants in food and laundry industry. Herein, we investigated the interaction of three surfactants (sodium dodecyl sulfate (SDS), sodium dodecyl benzene sulfonate (SDBS), sodium lauryl sulfonate (SLS)) with Candida rugosa lipase (CRL), which is a popular biocatalyst used regularly with surfactants. The effect of the three surfactants on the conformation and activity of CRL was evaluated by using multiple spectral methods, enzyme activity assay and molecular docking modeling. The results demonstrated that CRL interacted with SDS, SDBS and SLS primarily through hydrophobic forces, H-bonding and electrostatic forces, respectively. The binding constants (K A ) of SDBS with CRL varied with temperature: 1.99×10 3 mol/L at 298K and 4.13×10 3 mol/L at 318K. SDS and SDBS affected the secondary structure and skeleton of CRL, which changed the polarity of CRL and enhanced its activity. SLS also changed the secondary structure and activity of CRL moderately, but had little effect on its polarity and chromophore microenvironment. Accordingly, all three surfactants exhibited effect to CRL on the molecular level calling for more attention to pay on their biosafety. The work demonstrates that SDS, SDBS and SLS could cause negative effects to CRL from different angles and therefore are not bio-friendly detergents. Copyright © 2017 Elsevier B.V. All rights reserved.

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

Work Integration of People with Disabilities in the Regular Labour Market: What Can We Do to Improve These Processes?

ERIC Educational Resources Information Center

Vila, Montserrat; Pallisera, Maria; Fullana, Judit

2007-01-01

Background: It is important to ensure that regular processes of labour market integration are available for all citizens. Method: Thematic content analysis techniques, using semi-structured group interviews, were used to identify the principal elements contributing to the processes of integrating people with disabilities into the regular labour…

Shape regularized active contour based on dynamic programming for anatomical structure segmentation

NASA Astrophysics Data System (ADS)

Yu, Tianli; Luo, Jiebo; Singhal, Amit; Ahuja, Narendra

2005-04-01

We present a method to incorporate nonlinear shape prior constraints into segmenting different anatomical structures in medical images. Kernel space density estimation (KSDE) is used to derive the nonlinear shape statistics and enable building a single model for a class of objects with nonlinearly varying shapes. The object contour is coerced by image-based energy into the correct shape sub-distribution (e.g., left or right lung), without the need for model selection. In contrast to an earlier algorithm that uses a local gradient-descent search (susceptible to local minima), we propose an algorithm that iterates between dynamic programming (DP) and shape regularization. DP is capable of finding an optimal contour in the search space that maximizes a cost function related to the difference between the interior and exterior of the object. To enforce the nonlinear shape prior, we propose two shape regularization methods, global and local regularization. Global regularization is applied after each DP search to move the entire shape vector in the shape space in a gradient descent fashion to the position of probable shapes learned from training. The regularized shape is used as the starting shape for the next iteration. Local regularization is accomplished through modifying the search space of the DP. The modified search space only allows a certain amount of deformation of the local shape from the starting shape. Both regularization methods ensure the consistency between the resulted shape with the training shapes, while still preserving DP"s ability to search over a large range and avoid local minima. Our algorithm was applied to two different segmentation tasks for radiographic images: lung field and clavicle segmentation. Both applications have shown that our method is effective and versatile in segmenting various anatomical structures under prior shape constraints; and it is robust to noise and local minima caused by clutter (e.g., blood vessels) and other similar structures (e.g., ribs). We believe that the proposed algorithm represents a major step in the paradigm shift to object segmentation under nonlinear shape constraints.

Cross-sectional study to evaluate the associated factors with differences between city and districts secondary school students of the southeast of Spain (Murcia) for their adherence to the Mediterranean diet.

PubMed

Doménech-Asensi, Guillermo; Sánchez-Martínez, Álvaro; Ros-Berruezo, Gaspar

2014-12-17

The "Mediterranean diet" is recognized as one of the healthiest dietary patterns but, even in Mediterranean countries it is gradually being lost. Adolescence is a crucial period for changes in dietary patterns. The purpose of this study was to evaluate the Adherence to Mediterranean diet (AMD) of secondary school students and evaluate possible variations between those residents in the city or in the districts. A cross-sectional study was designed with 379 secondary school students. To assess the AMD a self-administered questionnaire KIDMED was used. They were classified according to sex and residence (city or districts). The body mass index (BMI) for the whole sample was 22.34 in boys and 20.79 in girls (p<0.05). Students from the city resulted more physically active than those from the districts (p<0.05). The average AMD score was 5.8, with 20.3% of students showing good adherence. In general, there was a low consumption of fruits, vegetables and pasta or rice, all foods included in the bottom of the dietary pyramid and the consumption of olive oil and legumes was very positive. Around 25% of students skip breakfast regularly. Although BMI was in general in the range of normality, AMD of secondary school students is lower than expected attending to previous studies. Consume of fruits and vegetables several times per day, having breakfast daily and regular physical activity should be promoted. Educational and informative activities should be designed for adolescents and also for their parents since in these stages menus at home are usually established by them. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

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.

[Effect of measures for the detection and long-term drug therapy of arterial hypertension on the morbidity and work capacity of industrial workers].

PubMed

Evdakov, V A; Baĭda, S M; Britov, A N; Safronova, M B; Grigor'eva, N V

1985-01-01

The article contains data on preliminary evaluation of the efficacy of secondary prevention of arterial hypertension among industrial workers of "Avto ZIL" amalgamation. Population studies to reveal major cardiovascular diseases show a certain increase of arterial hypertension and other disease morbidity accompanied by temporary disability. A considerable positive effect is observed in groups of hypertensives undergoing regular and effective anti-hypertension preventive treatment. Long-term regular hypotensive treatment of hypertensive subjects and the lowering of blood pressure to less than 160/90 mm Hg contributes to the decrease in labour and economic losses and to increased labour productivity of industrial workers.

Life threatening hyperkalemia and acidosis secondary to trimethoprim-sulfamethoxazole treatment.

PubMed

Margassery, S; Bastani, B

2001-01-01

We present a 77-year-old male with moderate chronic renal insufficiency from diabetic nephropathy who developed severe metabolic acidosis and life threatening hyperkalemia on treatment with regular dose of trimethoprim-sulfamethoxazole (TMP-SMZ) for urinary tract infection. The metabolic acidosis and hyperkalemia resolved upon appropriate medical intervention and discontinuation of TMP-SMZ. While hyperkalemia has commonly been reported with high dose of TMP-SMZ, severe metabolic acidosis is quite uncommon with regular dose TMP-SMZ. We emphasize that patients with renal tubular acidosis (RTA), renal insufficiency, aldosterone deficiency, old age with reduced renal mass and function, and angiotensin converting enzyme (ACE)-inhibitor therapy are at high risk of developing these severe and potentially life threatening complications.

Integrated Occupational Program: Information Manual for Administrators, Counsellors, and Teachers. Interim 1988.

ERIC Educational Resources Information Center

Forest, Jan

The Integrated Occupational Program (IOP) was designed for students in grades 8-12 who have experienced prolonged difficulty with the regular elementary and secondary school programs, who demonstrate a significant lag in one or more of their academic courses, and who typically fall into the intelligence band of 75-95 IQ. The IOP enables students…

The Adoption of "Thinking through Geography" Strategies and Their Impact on Teaching Geographical Reasoning in Dutch Secondary Schools

ERIC Educational Resources Information Center

Hooghuis, Fer; van der Schee, Joop; van der Velde, Martin; Imants, Jeroen; Volman, Monique

2014-01-01

The development of geographical reasoning is essential in geographical education. Strategies developed by the English "Thinking Through Geography" group (TTG) offer a promising approach to promote geographical reasoning. In the last decade, the TTG approach has become a regular element in geographical education in several countries.…

Compensatory Education Product Evaluation: Elementary and Secondary Programs 1991-1992.

ERIC Educational Resources Information Center

Saginaw Public Schools, MI. Dept. of Evaluation Services.

An evaluation was done of compensatory educational programs in reading and mathematics in the Saginaw (Michigan) School District. The elementary Compensatory Education (CE) program is both a push-in format (grades 1 and 2) and a pull-out format (periodically taking students out of regular classrooms) that serves 2,045 students in grades 1 through…

Visibly Learning: Teachers' Assessment Practices for Students with High and Very High Needs

ERIC Educational Resources Information Center

Bourke, Roseanna; Mentis, Mandia; Todd, Liz

2011-01-01

This paper examines the assessment practices of teachers working with students with special educational needs in New Zealand primary and secondary regular and special schools. A national survey was used to identify current assessment practices used by teachers working with students designated, through a resourcing policy, as having high and very…

Characteristics of Public School Teachers' Professional Development Activities: 1999-2000. NCES Issue Brief. NCES 2005-030

ERIC Educational Resources Information Center

Scotchmer, Marion; McGrath, Daniel J.; Coder, Ellinor

2005-01-01

As in many professions, elementary and secondary school teachers are expected to participate regularly in professional development activities. These activities may be intended to help teachers to learn new teaching methods, broaden their subject matter content knowledge, or stay informed of changing policies, among other purposes. Researchers have…

1981 Maryland Migrant Education State Plan.

ERIC Educational Resources Information Center

Friend, Ronn E.; Gates, Francis W.

Between October 1, 1980 and September 30, 1981, the 1981 migrant education program will serve an estimated 1,109 migrant children in 6 regular and 8 summer school projects in Maryland. Of these children, 422 will be at the elementary level, 366 at the secondary level, and the rest will be in preschool. Blacks compose the largest ethnic group (478)…

Allowing Idiosyncratic Learners to Thrive: Policy Implications of a Study of School-within-a-School Gifted Programs

ERIC Educational Resources Information Center

Matthews, Dona; Kitchen, Julian

2007-01-01

School-within-a-school programs are an alternative school choice that can provide differentiated learning opportunities for academically gifted students, but they are often politically contentious. In a recent study, we interviewed 530 students and teachers in gifted and regular streams in three publicly funded secondary schools with different…

The Characteristics of "Mobile" and "Stable" Occupational Educators by Specialty and by Type of School.

ERIC Educational Resources Information Center

Wiens, A. Emerson

To generate information relative to job mobility which could be helpful to occupational administrators in hiring and meeting in-service education needs, questionnaires were sent to a two percent representative sampling of occupational educators in the U.S. The sample was divided by type of school (regular and comprehensive, secondary and…

A Study of Current In-School Suspension Programs in New York State.

ERIC Educational Resources Information Center

Foster, Herbert L.; Kight, Howard R.

In-school suspension (ISS) removes a student from regular academic classes but keeps the student in an isolated, separate, and restricted environment where, in most cases, academic work continues. Such programs have increased rapidly in American secondary schools, and have been mandated in New York State by the New York State Education Department…

Special Education Instructional Skills Guide for Identifiable Perceptual or Communicative Disorders (IPCD) and Significant Identifiable Emotional or Behavioral Disorders (SIEBD) K-12.

ERIC Educational Resources Information Center

George-Nichols, Nancy; And Others

The guide is intended to provide information on appropriate programing for elementary and secondary pupils with either perceptual/communicative or emotional/behavioral disorders. The guide, which is patterned after regular education objectives, offers comprehensive task analysis in four content areas (subtopics in parentheses): (1) readiness…

Inclusion of Children with Special Needs in Early Childhood Education: What Teacher Characteristics Matter

ERIC Educational Resources Information Center

Lee, Frances Lai Mui; Yeung, Alexander Seeshing; Tracey, Danielle; Barker, Katrina

2015-01-01

Whereas the inclusion of children with special needs in regular classrooms has gained increasing advocacy, teachers' attitudes vary. Previous studies examining teacher attitudes have focused on primary and secondary schools in the Western world, and little is known about early childhood settings in Eastern countries. This study used MANOVA to…

The World and the School: A Review for Teachers of Current International Affairs, Number 19.

ERIC Educational Resources Information Center

Critchley, Julian

1970-01-01

The British Journal (triannual) is written for secondary level teachers of current international affairs. Typical format consists of a teaching topic with several analytical articles followed by others explaining how best to teach the concepts. Other regular sections include a four month summary of international events, articles on educational…

Recent Developments in Career Education in the Netherlands: Learning by Experience and Value Stimulation.

ERIC Educational Resources Information Center

Hofmeister, Jane; Veugelers, Wiel

Career education in the Netherlands is a regular part of the curriculum and provides students the opportunity to collect information about different professions and studies. The policy of the Dutch administration is to stimulate the creation of secondary schools with both vocational and academic tracks. Career education is designed to balance…

Conceptual Learning in Relation to Near and Far Transfer in the Secondary School Subject of Economics

ERIC Educational Resources Information Center

Kneppers, Lenie; Elshout-Mohr, Marianne; van Boxtel, Carla; van Hout-Wolters, Bernadette

2007-01-01

In this study we investigated the effects of two treatments supplementing students' (16 to 18 years of age and in pre-university education) regular course in economics. One treatment, labelled concept treatment, aimed at the solidification of the students' knowledge about economic concepts and their interrelations. The other treatment, labeled…

Soap Films and GeoGebra in the Study of Fermat and Steiner Points

ERIC Educational Resources Information Center

Flores, Alfinio; Park, Jungeun

2018-01-01

We discuss how mathematics and secondary mathematics education majors developed an understanding of Fermat points for the triangle as well as Steiner points for the square and regular pentagon, and also of soap film configurations between parallel plates where forces are in equilibrium. The activities included the use of soap films and the…

Computers in My Curriculum? 18 Lesson Plans for Teaching Computer Awareness without a Computer. Adaptable Grades 3-12.

ERIC Educational Resources Information Center

Bailey, Suzanne Powers; Jeffers, Marcia

Eighteen interrelated, sequential lesson plans and supporting materials for teaching computer literacy at the elementary and secondary levels are presented. The activities, intended to be infused into the regular curriculum, do not require the use of a computer. The introduction presents background information on computer literacy, suggests a…

A stewardship approach to grassland bird habitat conservation in Saskatchewan, Canada

Treesearch

Stephen K. Davis; Bob Springer; Jennifer Lohmeyer; Lesley Hall; Tom Harrison

2005-01-01

Saskatchewan provides habitat for a number of grassland specialists that are of high conservation concern. For example, 10 of 12 “primary endemic,” and 17 of 25 “secondary endemic” species of the Great Plains identified by Mengel (1970) regularly breed in Saskatchewan. In addition, each of the 30 species of high conservation...

Paired Reading: Evaluation Report and Executive Summary

ERIC Educational Resources Information Center

Lloyd, Cheryl; Edovald, Triin; Kiss, Zsolt; Morris, Stephen; Skipp, Amy; Ahmed, Hashim

2015-01-01

Paired Reading is a peer tutoring programme in secondary schools which trains teachers to support and encourage the regular tutoring of Year 7 pupils (aged 11-12 years) by Year 9 pupils (aged 13-14 years). The Paired Reading programme aims to improve pupils' general literacy in addition to speaking and listening skills. This is achieved by pupils…

A Longitudinal Assessment of Early Acceleration of Students in Mathematics on Growth in Mathematics Achievement

ERIC Educational Resources Information Center

Ma, X.

2005-01-01

Early acceleration of students in mathematics (in the form of early access to formal abstract algebra) has been a controversial educational issue. The current study examined the rate of growth in mathematics achievement of accelerated gifted, honors, and regular students across the entire secondary years (Grades 7-12), in comparison to their…

Public Perceptions, Private Agendas: Washington, Moton, and the Secondary Curriculum of Tuskegee Institute 1910-1926

ERIC Educational Resources Information Center

Morowski, Deborah L.

2013-01-01

After the Civil War, schooling for African Americans was irregular and consisted mainly of elementary grades. Education was provided, primarily, by elite, private institutions and fewer than three percent of students aged 13-17 attended regularly. In 1896, the United States Supreme Court issued a ruling in "Plessey v. Ferguson." Although…

Incorporation of Consumer Education [Lessons] in Adult Basic Education Programs in North Dakota. Final Report.

ERIC Educational Resources Information Center

Shurr, Harriet

Two North Dakota home economists developed consumer education curricula based on adult performance level (APL) objectives and the perceived needs of their vocational students. They worked with local directors of adult basic and secondary education (ABSE) to incorporate the curricula into regular ABSE classes. Project objectives were to (1)…

Content-Based Instruction in Primary and Secondary School Settings. Case Studies in TESOL Practice Series

ERIC Educational Resources Information Center

Kaufman, Dorit, Ed.; Crandall, JoAnn, Ed.

2005-01-01

Content-based instruction (CBI) challenges English language educators to teach English using materials that learners encounter in their regular subject-area classes. This volume helps ESL and EFL teachers meet that challenge by providing them with creative ways to integrate English language learning with the content that students study at primary…

Regularization of the Perturbed Spatial Restricted Three-Body Problem by L-Transformations

NASA Astrophysics Data System (ADS)

Poleshchikov, S. M.

2018-03-01

Equations of motion for the perturbed circular restricted three-body problem have been regularized in canonical variables in a moving coordinate system. Two different L-matrices of the fourth order are used in the regularization. Conditions for generalized symplecticity of the constructed transform have been checked. In the unperturbed case, the regular equations have a polynomial structure. The regular equations have been numerically integrated using the Runge-Kutta-Fehlberg method. The results of numerical experiments are given for the Earth-Moon system parameters taking into account the perturbation of the Sun for different L-matrices.

Slice regular functions of several Clifford variables

NASA Astrophysics Data System (ADS)

Ghiloni, R.; Perotti, A.

2012-11-01

We introduce a class of slice regular functions of several Clifford variables. Our approach to the definition of slice functions is based on the concept of stem functions of several variables and on the introduction on real Clifford algebras of a family of commuting complex structures. The class of slice regular functions include, in particular, the family of (ordered) polynomials in several Clifford variables. We prove some basic properties of slice and slice regular functions and give examples to illustrate this function theory. In particular, we give integral representation formulas for slice regular functions and a Hartogs type extension result.

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

Regularization and Approximation of a Class of Evolution Problems in Applied Mathematics

DTIC Science & Technology

1991-01-01

8217 DT)IG AD-A242 223 FINAL REPORT Nov61991:ti -ll IN IImI 1OV1 Ml99 1 REGULARIZATION AND APPROXIMATION OF A-CLASS OF EVOLUTION -PROBLEMS IN APPLIED...The University of Texas at Austin Austin, TX 78712 91 10 30 050 FINAL REPORT "Regularization and Approximation of a Class of Evolution Problems in...micro-structured parabolic system. A mathematical analysis of the regularized equations-has been developed to support our approach. Supporting

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.

Electroluminescence of fluorescent-phosphorescent organic light-emitting diodes with regular, inverted, and symmetrical structures

NASA Astrophysics Data System (ADS)

Yang, Su-Hua; Shih, Po-Jen; Wu, Wen-Jie

2014-11-01

The influence of the device structure on the electroluminescence (EL) properties of fluorescent-phosphorescent organic light emitting diodes (OLEDs) was demonstrated. Four devices with regular-, inverted-, compensated- and symmetrical-emission layers (EMLs) were prepared. In regular-EML device, DCJTB emission increased when the phosphorescent sensitized EML was thickened. In inverted-EML device, low electron energy barrier at the Bphen/BCzVB interface resulted in weakened blue emission. The compensated-EML device, prepared with a red color-compensated layer, showed a color-tunable broadband white emission. Conversely, device with a quantum-like symmetrical-EML showed a narrow color-temperature range. Stable EL efficiency was obtained from regular, compensated, and symmetrical-EML devices. In contrast, EL efficiency of inverted-EML device rolled off significantly, though it had the highest EL efficiency of 11.4 cd/A.

Traveling wave linear accelerator with RF power flow outside of accelerating cavities

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

Dolgashev, Valery A.

A high power RF traveling wave accelerator structure includes a symmetric RF feed, an input matching cell coupled to the symmetric RF feed, a sequence of regular accelerating cavities coupled to the input matching cell at an input beam pipe end of the sequence, one or more waveguides parallel to and coupled to the sequence of regular accelerating cavities, an output matching cell coupled to the sequence of regular accelerating cavities at an output beam pipe end of the sequence, and output waveguide circuit or RF loads coupled to the output matching cell. Each of the regular accelerating cavities hasmore » a nose cone that cuts off field propagating into the beam pipe and therefore all power flows in a traveling wave along the structure in the waveguide.« less

Phenologic variation of major triterpenoids in regular and white Antrodia cinnamomea.

PubMed

Chen, Wei-Lun; Ho, Yen-Peng; Chou, Jyh-Ching

2016-12-01

Antrodia cinnamomea and its host Cinnamomum kanehirae are both endemic species unique to Taiwan. Many studies have confirmed that A. cinnamomea is rich in polysaccharides and triterpenoids that may carry medicinal effects in anti-cancer, anti-inflammation, anti-hypertension, and anti-oxidation. Therefore it is of interest to study the chemical variation of regular orange-red strains and white strains, which included naturally occurring and blue-light induced white A. cinnamomea. The chemical profiles of A. cinnamomea extracts at different growth stages were compared using thin layer chromatography (TLC) and high performance liquid chromatography (HPLC). The TLC and HPLC profiles indicated that specific triterpenoids varied between white and regular strains. Moreover, the compounds of blue-light induced white strain were similar to those of naturally occurring white strain but retained specific chemical characteristics in more polar region of the HPLC chromatogram of regular strain. Blue-light radiation could change color of the regular A. cinnamomea from orange-red to white by changing its secondary metabolism and growth condition. Naturally occurring white strain did not show a significantly different composition of triterpenoid profiles up to eight weeks old when compared with the triterpenoid profiles of the regular strain at the same age. The ergostane-type triterpenoids were found existing in both young mycelia and old mycelia with fruiting body in artificial agar-plate medium culture, suggesting a more diversified biosynthetic pathway in artificial agar-plate culture rather than wild or submerged culture.

Optimal Tikhonov Regularization in Finite-Frequency Tomography

NASA Astrophysics Data System (ADS)

Fang, Y.; Yao, Z.; Zhou, Y.

2017-12-01

The last decade has witnessed a progressive transition in seismic tomography from ray theory to finite-frequency theory which overcomes the resolution limit of the high-frequency approximation in ray theory. In addition to approximations in wave propagation physics, a main difference between ray-theoretical tomography and finite-frequency tomography is the sparseness of the associated sensitivity matrix. It is well known that seismic tomographic problems are ill-posed and regularizations such as damping and smoothing are often applied to analyze the tradeoff between data misfit and model uncertainty. The regularizations depend on the structure of the matrix as well as noise level of the data. Cross-validation has been used to constrain data uncertainties in body-wave finite-frequency inversions when measurements at multiple frequencies are available to invert for a common structure. In this study, we explore an optimal Tikhonov regularization in surface-wave phase-velocity tomography based on minimization of an empirical Bayes risk function using theoretical training datasets. We exploit the structure of the sensitivity matrix in the framework of singular value decomposition (SVD) which also allows for the calculation of complete resolution matrix. We compare the optimal Tikhonov regularization in finite-frequency tomography with traditional tradeo-off analysis using surface wave dispersion measurements from global as well as regional studies.

Gift from statistical learning: Visual statistical learning enhances memory for sequence elements and impairs memory for items that disrupt regularities.

PubMed

Otsuka, Sachio; Saiki, Jun

2016-02-01

Prior studies have shown that visual statistical learning (VSL) enhances familiarity (a type of memory) of sequences. How do statistical regularities influence the processing of each triplet element and inserted distractors that disrupt the regularity? Given that increased attention to triplets induced by VSL and inhibition of unattended triplets, we predicted that VSL would promote memory for each triplet constituent, and degrade memory for inserted stimuli. Across the first two experiments, we found that objects from structured sequences were more likely to be remembered than objects from random sequences, and that letters (Experiment 1) or objects (Experiment 2) inserted into structured sequences were less likely to be remembered than those inserted into random sequences. In the subsequent two experiments, we examined an alternative account for our results, whereby the difference in memory for inserted items between structured and random conditions is due to individuation of items within random sequences. Our findings replicated even when control letters (Experiment 3A) or objects (Experiment 3B) were presented before or after, rather than inserted into, random sequences. Our findings suggest that statistical learning enhances memory for each item in a regular set and impairs memory for items that disrupt the regularity. Copyright © 2015 Elsevier B.V. All rights reserved.

Direct Recordings of Pitch Responses from Human Auditory Cortex

PubMed Central

Griffiths, Timothy D.; Kumar, Sukhbinder; Sedley, William; Nourski, Kirill V.; Kawasaki, Hiroto; Oya, Hiroyuki; Patterson, Roy D.; Brugge, John F.; Howard, Matthew A.

2010-01-01

Summary Pitch is a fundamental percept with a complex relationship to the associated sound structure [1]. Pitch perception requires brain representation of both the structure of the stimulus and the pitch that is perceived. We describe direct recordings of local field potentials from human auditory cortex made while subjects perceived the transition between noise and a noise with a regular repetitive structure in the time domain at the millisecond level called regular-interval noise (RIN) [2]. RIN is perceived to have a pitch when the rate is above the lower limit of pitch [3], at approximately 30 Hz. Sustained time-locked responses are observed to be related to the temporal regularity of the stimulus, commonly emphasized as a relevant stimulus feature in models of pitch perception (e.g., [1]). Sustained oscillatory responses are also demonstrated in the high gamma range (80–120 Hz). The regularity responses occur irrespective of whether the response is associated with pitch perception. In contrast, the oscillatory responses only occur for pitch. Both responses occur in primary auditory cortex and adjacent nonprimary areas. The research suggests that two types of pitch-related activity occur in humans in early auditory cortex: time-locked neural correlates of stimulus regularity and an oscillatory response related to the pitch percept. PMID:20605456

Effects of repeated doses of caffeine on performance and alertness: new data and secondary analyses.

PubMed

Hewlett, Paul; Smith, Andrew

2007-08-01

The effects of caffeine on mood and performance are well established. Some authors suggest that caffeine merely reverses effects of caffeine withdrawal rather than having direct behavioural effects. It has also been suggested that withdrawal may be removed by a first dose of caffeine and further doses have little subsequent effect. These issues are examined here. The present study aimed to determine whether caffeine withdrawal influenced mood and performance by comparing regular consumers who had been withdrawn from caffeine overnight with non-consumers. Following this repeated caffeine doses were administered to test the claim that repeated dosing has no extra effect on mood or performance. Secondary analyses of data collected after a day of normal caffeine consumption were also carried out to examine some alternative explanations of their results which showed effects of caffeine after a day of normal caffeine consumption. One hundred and twenty volunteers participated in the study. Regular caffeine consumption was assessed by questionnaire and this showed that 36 of the volunteers did not regularly consume caffeinated beverages. Volunteers were instructed to abstain from caffeine overnight and then completed a baseline session measuring mood and a range of cognitive functions at 08.00 the next day. Following this volunteers were given 0, or 1 mg/kg caffeine in a milkshake, glucose solution or water (at 09:00), followed by a second 0 or 1 mg/kg caffeine dose (at 09:40) and the test battery repeated at 10:00. The baseline data showed no effect of overnight caffeine withdrawal on mood or performance. In contrast, caffeine challenge improved vigilance performance and prevented decreases in alertness induced by completion of the task battery. The magnitude of these effects increased as a function of the number of doses of caffeine given. Secondary analyses of data from Christopher et al. (2003) also confirmed that effects of caffeine did not depend on length of withdrawal. The present findings show no effect of overnight caffeine withdrawal on mood and performance. Caffeine challenge did have the predicted effect on alertness and vigilance, with the size of the effects increasing with caffeine dose. These findings suggest that the effects of caffeine are not due to reversal of effects of withdrawal, a view confirmed by secondary analyses of data collected after a day of normal caffeine consumption. Copyright 2007 John Wiley & Sons, Ltd.

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.

Regularity and Tresse's theorem for geometric structures

NASA Astrophysics Data System (ADS)

Sarkisyan, R. A.; Shandra, I. G.

2008-04-01

For any non-special bundle P\\to X of geometric structures we prove that the k-jet space J^k of this bundle with an appropriate k contains an open dense domain U_k on which Tresse's theorem holds. For every s\\geq k we prove that the pre-image \\pi^{-1}(k,s)(U_k) of U_k under the natural projection \\pi(k,s)\\colon J^s\\to J^k consists of regular points. (A point of J^s is said to be regular if the orbits of the group of diffeomorphisms induced from X have locally constant dimension in a neighbourhood of this point.)

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

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.

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

The crown splash

NASA Astrophysics Data System (ADS)

Deegan, Robert; Brunet, Philippe; Eggers, Jens

2008-11-01

The impact of a drop onto a liquid layer and the subsequent splash has important implications for diverse physical processes such as air-sea gas transfer, cooling, and combustion. In the crown splash parameter regime, the splash pattern is highly regular. We focus on this case as a model for the mechanism that leads to secondary droplets, and thus explain the drop size distribution resulting from the splash. We show that the mean number of secondary droplets is determined by the most unstable wavelength of the Rayleigh-Plateau instability. Variations from this mean are governed by the width of the spectrum. Our results for the crown splash will provide the basis for understanding more complicated splashes.

Multifractal surrogate-data generation algorithm that preserves pointwise Hölder regularity structure, with initial applications to turbulence

NASA Astrophysics Data System (ADS)

Keylock, C. J.

2017-03-01

An algorithm is described that can generate random variants of a time series while preserving the probability distribution of original values and the pointwise Hölder regularity. Thus, it preserves the multifractal properties of the data. Our algorithm is similar in principle to well-known algorithms based on the preservation of the Fourier amplitude spectrum and original values of a time series. However, it is underpinned by a dual-tree complex wavelet transform rather than a Fourier transform. Our method, which we term the iterated amplitude adjusted wavelet transform can be used to generate bootstrapped versions of multifractal data, and because it preserves the pointwise Hölder regularity but not the local Hölder regularity, it can be used to test hypotheses concerning the presence of oscillating singularities in a time series, an important feature of turbulence and econophysics data. Because the locations of the data values are randomized with respect to the multifractal structure, hypotheses about their mutual coupling can be tested, which is important for the velocity-intermittency structure of turbulence and self-regulating processes.

Spatio-Temporal Regularization for Longitudinal Registration to Subject-Specific 3d Template

PubMed Central

Guizard, Nicolas; Fonov, Vladimir S.; García-Lorenzo, Daniel; Nakamura, Kunio; Aubert-Broche, Bérengère; Collins, D. Louis

2015-01-01

Neurodegenerative diseases such as Alzheimer's disease present subtle anatomical brain changes before the appearance of clinical symptoms. Manual structure segmentation is long and tedious and although automatic methods exist, they are often performed in a cross-sectional manner where each time-point is analyzed independently. With such analysis methods, bias, error and longitudinal noise may be introduced. Noise due to MR scanners and other physiological effects may also introduce variability in the measurement. We propose to use 4D non-linear registration with spatio-temporal regularization to correct for potential longitudinal inconsistencies in the context of structure segmentation. The major contribution of this article is the use of individual template creation with spatio-temporal regularization of the deformation fields for each subject. We validate our method with different sets of real MRI data, compare it to available longitudinal methods such as FreeSurfer, SPM12, QUARC, TBM, and KNBSI, and demonstrate that spatially local temporal regularization yields more consistent rates of change of global structures resulting in better statistical power to detect significant changes over time and between populations. PMID:26301716

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.

Peeling the onion: ribosomes are ancient molecular fossils.

PubMed

Hsiao, Chiaolong; Mohan, Srividya; Kalahar, Benson K; Williams, Loren Dean

2009-11-01

We describe a method to establish chronologies of ancient ribosomal evolution. The method uses structure-based and sequence-based comparison of the large subunits (LSUs) of Haloarcula marismortui and Thermus thermophilus. These are the highest resolution ribosome structures available and represent disparate regions of the evolutionary tree. We have sectioned the superimposed LSUs into concentric shells, like an onion, using the site of peptidyl transfer as the origin (the PT-origin). This spherical approximation combined with a shell-by-shell comparison captures significant information along the evolutionary time line revealing, for example, that sequence and conformational similarity of the 23S rRNAs are greatest near the PT-origin and diverge smoothly with distance from it. The results suggest that the conformation and interactions of both RNA and protein can be described as changing, in an observable manner, over evolutionary time. The tendency of macromolecules to assume regular secondary structural elements such as A-form helices with Watson-Crick base pairs (RNA) and alpha-helices and beta-sheets (protein) is low at early time points but increases as time progresses. The conformations of ribosomal protein components near the PT-origin suggest that they may be molecular fossils of the peptide ancestors of ribosomal proteins. Their abbreviated length may have proscribed formation of secondary structure, which is indeed nearly absent from the region of the LSU nearest the PT-origin. Formation and evolution of the early PT center may have involved Mg(2+)-mediated assembly of at least partially single-stranded RNA oligomers or polymers. As one moves from center to periphery, proteins appear to replace magnesium ions. The LSU is known to have undergone large-scale conformation changes upon assembly. The T. thermophilus LSU analyzed here is part of a fully assembled ribosome, whereas the H. marismortui LSU analyzed here is dissociated from other ribosomal components. Large-scale conformational differences in the 23S rRNAs are evident from superimposition and prevent structural alignment of some portions of the rRNAs, including the L1 stalk.

Examining the Potential of Critical and Kaupapa Maori Approaches to Leading Education Reform in New Zealand's English-Medium Secondary Schools

ERIC Educational Resources Information Center

Berryman, Mere; Egan, Margaret; Ford, Therese

2017-01-01

This paper discusses expectations, policies and practices that currently underpin education within the New Zealand context. It acknowledges the ongoing failure of this policy framework to positively influence reform for Indigenous Maori students in regular, state-funded schools and highlights the need for extensive change in the positioning and…

Homophobia in Secondary Schools: An Investigation of Teachers' Perceptions of Homophobia through a Collaborative Professional Development Program

ERIC Educational Resources Information Center

Jones, Joseph R.

2010-01-01

According to Gay Lesbian Straight Education Network, GLSEN, (2003), 84% of GLBT students experienced homophobic remarks or verbal harassment and of those, 91.5% reported hearing the word "faggot" or "dyke" on a regular basis, and over 60% felt unsafe in their schools because of their sexual orientation. More recently, several middle school…

That's so Homophobic? Australian Young People's Perspectives on Homophobic Language Use in Secondary Schools

ERIC Educational Resources Information Center

Fulcher, Karyn

2017-01-01

It is generally accepted that hearing homophobic language can be detrimental to the well-being of same-sex attracted young people. "Writing Themselves In 3," a survey of Australian same-sex attracted young people, found that almost half of the respondents reported hearing such language on a regular basis, and considered it offensive.…

Analysing the Correlation between Secondary Mathematics Curriculum Change and Trends in Beginning Undergraduates' Performance of Basic Mathematical Skills in Ireland

ERIC Educational Resources Information Center

Treacy, Páraic; Faulkner, Fiona; Prendergast, Mark

2016-01-01

The phenomenon in which students enter university under-prepared for the mathematical demands of their undergraduate courses, regularly referred to as the 'Maths Problem', has been widely reported in Ireland, UK, Australia, and the US. This issue has been of particular concern in Ireland recently, with beginning undergraduates' performance of…

The Lived Experiences of 24/7 Connectivity on Secondary Educators

ERIC Educational Resources Information Center

Heiden, James P.

2012-01-01

Student access to the Internet has dramatically increased during the first decade of 2000. A recent study indicated that over 85% of US teens have regular access to a cell phone (Rideout et al., 2010). The cell phone coupled with an Internet plan has created the smart phone. This technology allows students to decide when and where they want to…

VOC-PLAN: Individual Vocational Education Plan (A Quick, Efficient and Creative Way to Generate Vocational I.E.P.s), Users Manual and Preview Manual.

ERIC Educational Resources Information Center

Robinson, Jim; Seabolt, Pete

This User's Manual is intended to accompany VOC-PLAN, a computer (Apple) program designed to assist in the preparation of an Individualized Vocational Education Program (IVEP) for handicapped, disadvantaged, or regular vocational secondary and postsecondary students. The program is presented in standard IEP (Individualized Education Program)…

Secondary Education Teachers' Perceptions of Students with Autism Spectrum Disorder in the Regular Education Classroom

ERIC Educational Resources Information Center

Mahler, Crystal Lee

2016-01-01

The American Psychiatric Association (2000) defined Autism Spectrum Disorder (ASD) as a mild to severe neurological condition with unknown causes that affects the brain's sensory filters and social development. According to Rice (2009), the number of people diagnosed with autism has increased to one out of every 88 children. As a result of the…

Nearly Two Decades after the Implementation of Persons with Disabilities Act: Concerns of Indian Teachers to Implement Inclusive Education

ERIC Educational Resources Information Center

Bhatnagar, Nisha; Das, Ajay

2013-01-01

This study examined the concerns of regular secondary school teachers in Delhi, India in order to work with students with disabilities in inclusive education settings. A total of 470 teachers responded to a two-part questionnaire. Part-one of the questionnaire collected information related to personal and professional characteristics of the…

"Whatever Is Comfortable:" Secondary Physical Educators' Curricular Decision Making: Issues of Knowledge and Gendered Performativity

ERIC Educational Resources Information Center

Ferry, Matthew; McCaughtry, Nate

2015-01-01

Throughout history there have been debates as to what content knowledge (CK) is of most value for physical education (PE). Much recent conversation has circulated around the hope that time spent in PE supports students' regular participation in physical activity (PA). Researchers' use of the term PA, however, often stresses the similarities while…

A New Look at Some Pieces of Old Puzzles. Learnings from Schools and Teachers. Report No. 9016.

ERIC Educational Resources Information Center

Lieberman, Ann; Miller, Lynne

An overview is presented of research studies that reflect the realities that exist in elementary and secondary public education. Explorations of school culture cite behavioral and programmatic regularities that make up the school culture and the importance of school principals' roles. Focusing on the teachers and the ways things actually get done…

Woodworking Guide for Visually Handicapped Students. A Five County Vocational Skills Training Program for the Blind.

ERIC Educational Resources Information Center

Gaver, Wayne

Presented is an industrial arts curriculum guide for woodworking which developed out of a 3 year program designed to meet the unmet vocational education needs of visually impaired students enrolled in junior high, secondary, and community colleges in a five county region of California, and to provide inservice training to regular vocational…

One to Grow On. Chapter One in Ohio: Education Consolidation and Improvement Act.

ERIC Educational Resources Information Center

Douthitt, Frieda

Since 1965, first through Title I of the Elementary and Secondary Education Act and now through Chapter 1 of the Education Consolidation and Improvement Act, funds have been allocated to supplement regular classroom instruction for children achieving below grade level. Together, Title I and Chapter 1 form a 20-year continuum of a concentrated,…

"I Don't Have Time to Be This Busy." Exploring the Concerns of Secondary School Teachers Towards Inclusive Education

ERIC Educational Resources Information Center

Round, Penny N.; Subban, Pearl K.; Sharma, Umesh

2016-01-01

The trend towards inclusion in mainstream Australian schools has seen the numbers of students with disabilities educated in regular schools grow significantly. This trend has been supported by legislation such as the Disability Discrimination Act and the Education Standards. For inclusion to be successful, a number of factors are vital and teacher…

School soft drink availability and consumption among U.S. secondary students.

PubMed

Terry-McElrath, Yvonne M; O'Malley, Patrick M; Johnston, Lloyd D

2013-06-01

Consumption of sugar-sweetened beverages (SSBs) such as soft drinks has been associated with significantly increased energy intake and body weight. One strategy used to reduce soft drink consumption among adolescents has been reducing availability in schools; however, research is limited on associations between availability of soft drinks in school and student consumption. This study examines associations between regular and diet soft drink availability in schools and student consumption using data from 329 secondary schools and 9284 students. Data were obtained from two sources: (1) nationally representative cross-sectional samples of students in Grades 8, 10, and 12 from U.S. public and private schools in 2010 and 2011 in the Monitoring the Future study and (2) administrators of the same schools in the Youth, Education, and Society study. Multilevel modeling conducted in 2012 examined associations between school availability and student consumption controlling for student sociodemographics and school characteristics. In the total sample of more than 9000 students, regular and diet soft drink availability in school was not related to student consumption of these beverages in multivariate models. Yet, among African-American high school students, school regular and diet soft drink availability was significantly related to higher daily consumption (both before and after controlling for student and school factors). Although removal of soft drinks from schools may not result in significantly lower overall student consumption, such actions may result in significant decreases in soft drink consumption for specific student groups. Copyright © 2013 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

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.

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.

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

Self assembling proteins

DOEpatents

Yeates, Todd O.; Padilla, Jennifer; Colovos, Chris

2004-06-29

Novel fusion proteins capable of self-assembling into regular structures, as well as nucleic acids encoding the same, are provided. The subject fusion proteins comprise at least two oligomerization domains rigidly linked together, e.g. through an alpha helical linking group. Also provided are regular structures comprising a plurality of self-assembled fusion proteins of the subject invention, and methods for producing the same. The subject fusion proteins find use in the preparation of a variety of nanostructures, where such structures include: cages, shells, double-layer rings, two-dimensional layers, three-dimensional crystals, filaments, and tubes.

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

Linking imaging spectroscopy and trait data to better understand spatial and temporal variability in functional traits

NASA Astrophysics Data System (ADS)

Townsend, Philip; Kruger, Eric; Wang, Zhihui; Singh, Aditya

2017-04-01

Imaging spectroscopy exhibits great potential for mapping foliar functional traits that are impractical or expensive to regularly measure on the ground, and are essentially impossible to characterize comprehensively across space. Specifically, the high information content in spectroscopic data enables us to identify narrow spectral feature that are associated with vegetation primary and secondary biochemistry (nutrients, pigments, defensive compounds), leaf structure (e.g., leaf mass per area), canopy structure, and physiological capacity. Ultimately, knowledge of the variability in such traits is critical to understanding vegetation productivity, as well as responses to climatic variability, disturbances, pests and pathogens. The great challenge to the use of imaging spectroscopy to supplement trait databases is the development of trait retrieval approaches that are broadly applicable within and between ecosystem types. Here, we outline how we are using the US National Ecological Observatory Network (NEON) to prototype the scaling and comparison of trait distributions derived from field measurements and imagery. We find that algorithms to map traits from imagery are robust across ecosystem types, when controlling for physiognomy and vegetation percent cover, and that among all vegetation types, the chemometric algorithms utilize similar features for mapping of traits.

GIFTed Demons: deformable image registration with local structure-preserving regularization using supervoxels for liver applications

PubMed Central

Gleeson, Fergus V.; Brady, Michael; Schnabel, Julia A.

2018-01-01

Abstract. Deformable image registration, a key component of motion correction in medical imaging, needs to be efficient and provides plausible spatial transformations that reliably approximate biological aspects of complex human organ motion. Standard approaches, such as Demons registration, mostly use Gaussian regularization for organ motion, which, though computationally efficient, rule out their application to intrinsically more complex organ motions, such as sliding interfaces. We propose regularization of motion based on supervoxels, which provides an integrated discontinuity preserving prior for motions, such as sliding. More precisely, we replace Gaussian smoothing by fast, structure-preserving, guided filtering to provide efficient, locally adaptive regularization of the estimated displacement field. We illustrate the approach by applying it to estimate sliding motions at lung and liver interfaces on challenging four-dimensional computed tomography (CT) and dynamic contrast-enhanced magnetic resonance imaging datasets. The results show that guided filter-based regularization improves the accuracy of lung and liver motion correction as compared to Gaussian smoothing. Furthermore, our framework achieves state-of-the-art results on a publicly available CT liver dataset. PMID:29662918

GIFTed Demons: deformable image registration with local structure-preserving regularization using supervoxels for liver applications.

PubMed

Papież, Bartłomiej W; Franklin, James M; Heinrich, Mattias P; Gleeson, Fergus V; Brady, Michael; Schnabel, Julia A

2018-04-01

Deformable image registration, a key component of motion correction in medical imaging, needs to be efficient and provides plausible spatial transformations that reliably approximate biological aspects of complex human organ motion. Standard approaches, such as Demons registration, mostly use Gaussian regularization for organ motion, which, though computationally efficient, rule out their application to intrinsically more complex organ motions, such as sliding interfaces. We propose regularization of motion based on supervoxels, which provides an integrated discontinuity preserving prior for motions, such as sliding. More precisely, we replace Gaussian smoothing by fast, structure-preserving, guided filtering to provide efficient, locally adaptive regularization of the estimated displacement field. We illustrate the approach by applying it to estimate sliding motions at lung and liver interfaces on challenging four-dimensional computed tomography (CT) and dynamic contrast-enhanced magnetic resonance imaging datasets. The results show that guided filter-based regularization improves the accuracy of lung and liver motion correction as compared to Gaussian smoothing. Furthermore, our framework achieves state-of-the-art results on a publicly available CT liver dataset.

Manifold regularized multitask learning for semi-supervised multilabel image classification.

PubMed

Luo, Yong; Tao, Dacheng; Geng, Bo; Xu, Chao; Maybank, Stephen J

2013-02-01

It is a significant challenge to classify images with multiple labels by using only a small number of labeled samples. One option is to learn a binary classifier for each label and use manifold regularization to improve the classification performance by exploring the underlying geometric structure of the data distribution. However, such an approach does not perform well in practice when images from multiple concepts are represented by high-dimensional visual features. Thus, manifold regularization is insufficient to control the model complexity. In this paper, we propose a manifold regularized multitask learning (MRMTL) algorithm. MRMTL learns a discriminative subspace shared by multiple classification tasks by exploiting the common structure of these tasks. It effectively controls the model complexity because different tasks limit one another's search volume, and the manifold regularization ensures that the functions in the shared hypothesis space are smooth along the data manifold. We conduct extensive experiments, on the PASCAL VOC'07 dataset with 20 classes and the MIR dataset with 38 classes, by comparing MRMTL with popular image classification algorithms. The results suggest that MRMTL is effective for image classification.

Total variation regularization of the 3-D gravity inverse problem using a randomized generalized singular value decomposition

NASA Astrophysics Data System (ADS)

Vatankhah, Saeed; Renaut, Rosemary A.; Ardestani, Vahid E.

2018-04-01

We present a fast algorithm for the total variation regularization of the 3-D gravity inverse problem. Through imposition of the total variation regularization, subsurface structures presenting with sharp discontinuities are preserved better than when using a conventional minimum-structure inversion. The associated problem formulation for the regularization is nonlinear but can be solved using an iteratively reweighted least-squares algorithm. For small-scale problems the regularized least-squares problem at each iteration can be solved using the generalized singular value decomposition. This is not feasible for large-scale, or even moderate-scale, problems. Instead we introduce the use of a randomized generalized singular value decomposition in order to reduce the dimensions of the problem and provide an effective and efficient solution technique. For further efficiency an alternating direction algorithm is used to implement the total variation weighting operator within the iteratively reweighted least-squares algorithm. Presented results for synthetic examples demonstrate that the novel randomized decomposition provides good accuracy for reduced computational and memory demands as compared to use of classical approaches.

Assessment of Primary Health Care in the Treatment of Tuberculosis in a Brazilian Locality of the International Triple Frontier.

PubMed

Silva-Sobrinho, Reinaldo Antonio; Wysocki, Anneliese Domingues; Scatena, Lúcia Marina; Pinto, Erika Simone Galvão; Beraldo, Aline Ale; Andrade, Rubia Laine Paula; Zilly, Adriana; Munhak da Silva, Rosane Meire; Gomes, Michela Prestes; Mayer, Paulo César Morales; Ruffino-Netto, Antonio; Villa, Tereza Cristina Scatena

2017-01-01

To evaluate the performance of Primary Health Care (PHC) in treatment of TB patients in a triple international border municipality. The present study was an evaluative survey of cross-sectional and quantitative approach conducted with 225 PHC healthcare professionals. Data was collected through a structured and validated instrument, which provided five indicators of "structure" and four indicators of "process" classified as unsatisfactory, regular or satisfactory. The "structure" component was unsatisfactory for the indicator of professionals involved in TB care and training, and regular for the indicator of connection between the units and other levels of care. The "process" component was regular for the indicators of TB information, directly observed treatment and reference and counter reference on TB, and unsatisfactory for external actions on TB control. The "structure" and "process" components points out some weaknesses in terms of management and organization of human resources. Low frequency of training and the turnover influenced the involvement of professionals. Elements of "structure" and "process" show the need for investing in the PHC team and improving the clinical management of cases.

Seeking Temporal Predictability in Speech: Comparing Statistical Approaches on 18 World Languages

PubMed Central

Jadoul, Yannick; Ravignani, Andrea; Thompson, Bill; Filippi, Piera; de Boer, Bart

2016-01-01

Temporal regularities in speech, such as interdependencies in the timing of speech events, are thought to scaffold early acquisition of the building blocks in speech. By providing on-line clues to the location and duration of upcoming syllables, temporal structure may aid segmentation and clustering of continuous speech into separable units. This hypothesis tacitly assumes that learners exploit predictability in the temporal structure of speech. Existing measures of speech timing tend to focus on first-order regularities among adjacent units, and are overly sensitive to idiosyncrasies in the data they describe. Here, we compare several statistical methods on a sample of 18 languages, testing whether syllable occurrence is predictable over time. Rather than looking for differences between languages, we aim to find across languages (using clearly defined acoustic, rather than orthographic, measures), temporal predictability in the speech signal which could be exploited by a language learner. First, we analyse distributional regularities using two novel techniques: a Bayesian ideal learner analysis, and a simple distributional measure. Second, we model higher-order temporal structure—regularities arising in an ordered series of syllable timings—testing the hypothesis that non-adjacent temporal structures may explain the gap between subjectively-perceived temporal regularities, and the absence of universally-accepted lower-order objective measures. Together, our analyses provide limited evidence for predictability at different time scales, though higher-order predictability is difficult to reliably infer. We conclude that temporal predictability in speech may well arise from a combination of individually weak perceptual cues at multiple structural levels, but is challenging to pinpoint. PMID:27994544

Grade differences in reading motivation among Hong Kong primary and secondary students.

PubMed

Lau, Kit-Ling

2009-12-01

Most previous studies in Western societies have demonstrated a general decline in school motivation. However, it is not clear whether motivational decline occurs uniformly for all students. The moderating effects of individual and cultural differences on students' motivational decline need to be further explored. This study aimed to examine the grade differences in students' reading motivation, including self-efficacy, intrinsic motivation, extrinsic motivation, and social motivation, in a Chinese educational context. Grade by gender and grade by school-average achievement interactions were also checked to explore the role of individual differences in students' motivational changes. A total of 1,794 students (860 boys and 934 girls) volunteered to take part in this study, of whom 648 were Grade 4-6 students from 11 primary schools, 627 were Grade 7-9 students from 12 junior secondary schools, and 519 Grade 10-11 students from 6 senior secondary schools. A Chinese version of the Motivation for Reading Questionnaire (CRMQ) was administered to all participants during regular class periods by their teachers. Reliability analyses and confirmatory factor analysis (CFA) were first undertaken to assess the psychometric quality of the CRMQ. Then, multisample CFA was conducted to examine whether the factor structure of the CRMQ was equivalent across students at different grade levels. Grade differences in various reading motivation constructs as well as grade x gender and grade x school-average achievement interactions were examined using multiple-indicator-multiple-causes modelling. The findings of this study supported the reliability and the factor structure of the CRMQ in measuring the reading motivation of Chinese students at different grade levels. The factor pattern of the CRMQ was invariant across primary, junior secondary, and senior secondary students in multisample CFA. As far as the scores on the four reading motivation constructs were concerned, students scored most highly on intrinsic motivation, followed by self-efficacy, extrinsic motivation, and social motivation. Significant grade differences were found in all reading motivation constructs whereas only a few grade by gender and grade by school-average interactions were found. Consistent with previous studies in Western countries, the findings suggest that motivational decline is also a common phenomenon among Chinese students in Hong Kong. In addition, the pattern of motivational differences is generally consistent among students with different genders and from schools with different achievement levels. The implications of these findings for understanding Chinese students' reading motivation and for planning effective reading instruction to enhance their motivation are discussed.

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.

Basic Strategies for Mainstream Integration.

ERIC Educational Resources Information Center

Lawrence, Patrick A.

1988-01-01

Guidelines for effectively integrating learning-disabled or behavior problem students into regular classrooms are discussed. They include meetings between regular and special education teachers, class rules, discipline, clear directions, individualized instruction, direct instruction for skill acquisition, peer tutoring, structured activities,…

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.

Identification of moving vehicle forces on bridge structures via moving average Tikhonov regularization

NASA Astrophysics Data System (ADS)

Pan, Chu-Dong; Yu, Ling; Liu, Huan-Lin

2017-08-01

Traffic-induced moving force identification (MFI) is a typical inverse problem in the field of bridge structural health monitoring. Lots of regularization-based methods have been proposed for MFI. However, the MFI accuracy obtained from the existing methods is low when the moving forces enter into and exit a bridge deck due to low sensitivity of structural responses to the forces at these zones. To overcome this shortcoming, a novel moving average Tikhonov regularization method is proposed for MFI by combining with the moving average concepts. Firstly, the bridge-vehicle interaction moving force is assumed as a discrete finite signal with stable average value (DFS-SAV). Secondly, the reasonable signal feature of DFS-SAV is quantified and introduced for improving the penalty function (∣∣x∣∣2 2) defined in the classical Tikhonov regularization. Then, a feasible two-step strategy is proposed for selecting regularization parameter and balance coefficient defined in the improved penalty function. Finally, both numerical simulations on a simply-supported beam and laboratory experiments on a hollow tube beam are performed for assessing the accuracy and the feasibility of the proposed method. The illustrated results show that the moving forces can be accurately identified with a strong robustness. Some related issues, such as selection of moving window length, effect of different penalty functions, and effect of different car speeds, are discussed as well.

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

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

A novel type of light-harvesting antenna protein of red algal origin in algae with secondary plastids.

PubMed

Sturm, Sabine; Engelken, Johannes; Gruber, Ansgar; Vugrinec, Sascha; Kroth, Peter G; Adamska, Iwona; Lavaud, Johann

2013-07-30

Light, the driving force of photosynthesis, can be harmful when present in excess; therefore, any light harvesting system requires photoprotection. Members of the extended light-harvesting complex (LHC) protein superfamily are involved in light harvesting as well as in photoprotection and are found in the red and green plant lineages, with a complex distribution pattern of subfamilies in the different algal lineages. Here, we demonstrate that the recently discovered "red lineage chlorophyll a/b-binding-like proteins" (RedCAPs) form a monophyletic family within this protein superfamily. The occurrence of RedCAPs was found to be restricted to the red algal lineage, including red algae (with primary plastids) as well as cryptophytes, haptophytes and heterokontophytes (with secondary plastids of red algal origin). Expression of a full-length RedCAP:GFP fusion construct in the diatom Phaeodactylum tricornutum confirmed the predicted plastid localisation of RedCAPs. Furthermore, we observed that similarly to the fucoxanthin chlorophyll a/c-binding light-harvesting antenna proteins also RedCAP transcripts in diatoms were regulated in a diurnal way at standard light conditions and strongly repressed at high light intensities. The absence of RedCAPs from the green lineage implies that RedCAPs evolved in the red lineage after separation from the the green lineage. During the evolution of secondary plastids, RedCAP genes therefore must have been transferred from the nucleus of the endocytobiotic alga to the nucleus of the host cell, a process that involved complementation with pre-sequences allowing import of the gene product into the secondary plastid bound by four membranes. Based on light-dependent transcription and on localisation data, we propose that RedCAPs might participate in the light (intensity and quality)-dependent structural or functional reorganisation of the light-harvesting antennae of the photosystems upon dark to light shifts as regularly experienced by diatoms in nature. Remarkably, in plastids of the red lineage as well as in green lineage plastids, the phycobilisome based cyanobacterial light harvesting system has been replaced by light harvesting systems that are based on members of the extended LHC protein superfamily, either for one of the photosystems (PS I of red algae) or for both (diatoms). In their proposed function, the RedCAP protein family may thus have played a role in the evolutionary structural remodelling of light-harvesting antennae in the red lineage.

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.

A TPS kernel for calculating survival vs. depth: distributions in a carbon radiotherapy beam, based on Katz's cellular Track Structure Theory.

PubMed

Waligórski, M P R; Grzanka, L; Korcyl, M; Olko, P

2015-09-01

An algorithm was developed of a treatment planning system (TPS) kernel for carbon radiotherapy in which Katz's Track Structure Theory of cellular survival (TST) is applied as its radiobiology component. The physical beam model is based on available tabularised data, prepared by Monte Carlo simulations of a set of pristine carbon beams of different input energies. An optimisation tool developed for this purpose is used to find the composition of pristine carbon beams of input energies and fluences which delivers a pre-selected depth-dose distribution profile over the spread-out Bragg peak (SOBP) region. Using an extrapolation algorithm, energy-fluence spectra of the primary carbon ions and of all their secondary fragments are obtained over regular steps of beam depths. To obtain survival vs. depth distributions, the TST calculation is applied to the energy-fluence spectra of the mixed field of primary ions and of their secondary products at the given beam depths. Katz's TST offers a unique analytical and quantitative prediction of cell survival in such mixed ion fields. By optimising the pristine beam composition to a published depth-dose profile over the SOBP region of a carbon beam and using TST model parameters representing the survival of CHO (Chinese Hamster Ovary) cells in vitro, it was possible to satisfactorily reproduce a published data set of CHO cell survival vs. depth measurements after carbon ion irradiation. The authors also show by a TST calculation that 'biological dose' is neither linear nor additive. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field

NASA Astrophysics Data System (ADS)

Liwo, Adam; Czaplewski, Cezary; Pillardy, Jarosław; Scheraga, Harold A.

2001-08-01

A general method to derive site-site or united-residue potentials is presented. The basic principle of the method is the separation of the degrees of freedom of a system into the primary and secondary ones. The primary degrees of freedom describe the basic features of the system, while the secondary ones are averaged over when calculating the potential of mean force, which is hereafter referred to as the restricted free energy (RFE) function. The RFE can be factored into one-, two-, and multibody terms, using the cluster-cumulant expansion of Kubo. These factors can be assigned the functional forms of the corresponding lowest-order nonzero generalized cumulants, which can, in most cases, be evaluated analytically, after making some simplifying assumptions. This procedure to derive coarse-grain force fields is very valuable when applied to multibody terms, whose functional forms are hard to deduce in another way (e.g., from structural databases). After the functional forms have been derived, they can be parametrized based on the RFE surfaces of model systems obtained from all-atom models or on the statistics derived from structural databases. The approach has been applied to our united-residue force field for proteins. Analytical expressions were derived for the multibody terms pertaining to the correlation between local and electrostatic interactions within the polypeptide backbone; these expressions correspond to up to sixth-order terms in the cumulant expansion of the RFE. These expressions were subsequently parametrized by fitting to the RFEs of selected peptide fragments, calculated with the empirical conformational energy program for peptides force field. The new multibody terms enable not only the heretofore predictable α-helical segments, but also regular β-sheets, to form as the lowest-energy structures, as assessed by test calculations on a model helical protein A, as well as a model 20-residue polypeptide (betanova); the latter was not possible without introducing these new terms.

Metabolic and reward feeding synchronises the rhythmic brain.

PubMed

Challet, Etienne; Mendoza, Jorge

2010-07-01

Daily brain rhythmicity, which controls the sleep-wake cycle and neuroendocrine functions, is generated by an endogenous circadian timing system. Within the multi-oscillatory circadian network, a master clock is located in the suprachiasmatic nuclei of the hypothalamus, whose main synchroniser (Zeitgeber) is light. In contrast, imposed meal times and temporally restricted feeding are potent synchronisers for secondary clocks in peripheral organs such as the liver and in brain regions, although not for the suprachiasmatic nuclei. Even when animals are exposed to a light-dark cycle, timed calorie restriction (i.e. when only a hypocaloric diet is given every day) is a synchroniser powerful enough to modify the suprachiasmatic clockwork and increase the synchronising effects of light. A daily chocolate snack in animals fed ad libitum with chow diet entrains the suprachiasmatic clockwork only under the conditions of constant darkness and decreases the synchronising effects of light. Secondary clocks in the brain outside the suprachiasmatic nuclei are differentially influenced by meal timing. Circadian oscillations can either be highly sensitive to food-related metabolic or reward cues (i.e. their phase is shifted according to the timed meal schedule) in some structures or hardly affected by meal timing (palatable or not) in others. Furthermore, animals will manifest food-anticipatory activity prior to their expected meal time. Anticipation of a palatable or regular meal may rely on a network of brain clocks, involving metabolic and reward systems and the cerebellum.

A TRANSPLANTABLE NEW GROWTH OF THE FOWL, PRODUCING CARTILAGE AND BONE

PubMed Central

Tytler, W. H.

1913-01-01

An osteochondrosarcoma of the common fowl, designated in this laboratory as Chicken Tumor VII, has been successfully transplanted to seven successive series of hosts. The original growth contained bone and cartilage, was attached to the sternal keel of an otherwise healthy chicken, and appeared to have arisen from this structure. In the growths derived from its transplantation cartilage is regularly laid down, followed later by bone in case the host lives long enough. The prechondral tissue consists of spindle-shaped or multipolar cells of the fibroblast type. The histological character and the behavior of this prechondral tissue show that it is sarcomatous, a fact further proven by one recent case in which the tumor has metastasized. The secondary growth in this instance consisted of prechondral tissue in which a cartilaginous change was taking place. The tumor could not be transferred to pigeons, the one foreign species tested, but grew readily in chickens of two alien breeds. Reinoculation experiments suggest the occurrence of a natural, individual immunity, and of a certain degree of acquired resistance. In one fowl visceral growths developed following an intravenous injection of tumor emulsion, although whether they were due to this cause or were secondary to the large implantation growths in the muscles is uncertain. Recently the tumor has been transmitted by means of the filtrate from a Berkefeld filter. PMID:19867658

Teachers' stress intensifies violent disciplining in Tanzanian secondary schools.

PubMed

Hecker, Tobias; Goessmann, Katharina; Nkuba, Mabula; Hermenau, Katharin

2018-02-01

Violent forms of discipline in schools continue to be widespread across the globe despite their damaging effects. Since little is known about factors influencing the extent of violence applied by teachers, this study aimed to investigate the influence of teachers' stress, work satisfaction, and personal characteristics on their disciplining style. Using structural equation modeling, associations between violent discipline, burnout symptoms, and job perceptions (pressure and difficulties in class) reported by 222 teachers from 11 secondary schools in Tanzania in 2015 were analyzed. Results indicated a direct association between perceived stress and emotional violent discipline (β=.18, p<.05) as well as physical violent discipline (β=.37, p<.001). Perceived stress also mediated the association between job perceptions and both forms of violent disciplining. The model showed good model fit (χ 2 [44, n=222]=67.47 (p=.013), CFI=.94, TLI=.91, IFI=.94, RMSEA=.049 [90%-CI=.02-.07, PCLOSE=.50], SRMR=.06). Our findings suggest that teachers' personal perceptions of their work as well as their stress burden play a role in their disciplining styles. Our findings underline the importance of integrating topics, such as stress and coping as well as positive, nonviolent discipline measures into the regular teacher's training and in addition to develop and evaluate school-based preventative interventions for teachers. Copyright © 2017 Elsevier Ltd. All rights reserved.

A function space framework for structural total variation regularization with applications in inverse problems

NASA Astrophysics Data System (ADS)

Hintermüller, Michael; Holler, Martin; Papafitsoros, Kostas

2018-06-01

In this work, we introduce a function space setting for a wide class of structural/weighted total variation (TV) regularization methods motivated by their applications in inverse problems. In particular, we consider a regularizer that is the appropriate lower semi-continuous envelope (relaxation) of a suitable TV type functional initially defined for sufficiently smooth functions. We study examples where this relaxation can be expressed explicitly, and we also provide refinements for weighted TV for a wide range of weights. Since an integral characterization of the relaxation in function space is, in general, not always available, we show that, for a rather general linear inverse problems setting, instead of the classical Tikhonov regularization problem, one can equivalently solve a saddle-point problem where no a priori knowledge of an explicit formulation of the structural TV functional is needed. In particular, motivated by concrete applications, we deduce corresponding results for linear inverse problems with norm and Poisson log-likelihood data discrepancy terms. Finally, we provide proof-of-concept numerical examples where we solve the saddle-point problem for weighted TV denoising as well as for MR guided PET image reconstruction.

Can deformation of a polymer film with a rigid coating model geophysical processes?

NASA Astrophysics Data System (ADS)

Volynskii, A. L.; Bazhenov, S. L.

2007-12-01

The structural and mechanical behavior of polymer films with a thin rigid coating is analyzed. The behavior of such systems under applied stress is accompanied by the formation of a regular wavy surface relief and by regular fragmentation of the coating. The above phenomena are shown to be universal. Both phenomena (stress-induced development of a regular wavy surface relief and regular fragmentation of the coating) are provided by the specific features of mechanical stress transfer from a compliant soft support to a rigid thin coating. The above phenomena are associated with a specific structure of the system, which is referred to as “a rigid coating on a soft substratum” system (RCSS). Surface microrelief in RCSS systems is similar to the ocean floor relief in the vicinity of mid-oceanic ridges. Thus, the complex system composed of a young oceanic crust and upper Earth's mantle may be considered as typically “a solid coating on a soft substratum” system. Specific features of the ocean floor relief are analyzed in terms of the approach advanced for the description of the structural mechanical behavior of polymer films with a rigid coating. This analysis allowed to estimate the strength of an ocean floor.

Probing the cross-effect of strains in non-linear elasticity of nearly regular polymer networks by pure shear deformation.

PubMed

Katashima, Takuya; Urayama, Kenji; Chung, Ung-il; Sakai, Takamasa

2015-05-07

The pure shear deformation of the Tetra-polyethylene glycol gels reveals the presence of an explicit cross-effect of strains in the strain energy density function even for the polymer networks with nearly regular structure including no appreciable amount of structural defect such as trapped entanglement. This result is in contrast to the expectation of the classical Gaussian network model (Neo Hookean model), i.e., the vanishing of the cross effect in regular networks with no trapped entanglement. The results show that (1) the cross effect of strains is not dependent on the network-strand length; (2) the cross effect is not affected by the presence of non-network strands; (3) the cross effect is proportional to the network polymer concentration including both elastically effective and ineffective strands; (4) no cross effect is expected exclusively in zero limit of network concentration in real polymer networks. These features indicate that the real polymer networks with regular network structures have an explicit cross-effect of strains, which originates from some interaction between network strands (other than entanglement effect) such as nematic interaction, topological interaction, and excluded volume interaction.

Restrictions of physical activity participation in older adults with disability: employing keyword network analysis

PubMed Central

Koo, Kyo-Man; Kim, Chun-Jong; Park, Chae-Hee; Byeun, Jung-Kyun; Seo, Geon-Woo

2016-01-01

Older adults with disability might have been increasing due to the rapid aging of society. Many studies showed that physical activity is an essential part for improving quality of life in later lives. Regular physical activity is an efficient means that has roles of primary prevention and secondary prevention. However, there were few studies regarding older adults with disability and physical activity participation. The purpose of this current study was to investigate restriction factors to regularly participate older adults with disability in physical activity by employing keyword network analysis. Two hundred twenty-nine older adults with disability who were over 65 including aging with disability and disability with aging in type of physical disability and brain lesions defined by disabled person welfare law partook in the open questionnaire assessing barriers to participate in physical activity. The results showed that the keyword the most often used was ‘Traffic’ which was total of 21 times (3.47%) and the same proportion as in the ‘personal’ and ‘economical’. Exercise was considered the most central keyword for participating in physical activity and keywords such as facility, physical activity, disabled, program, transportation, gym, discomfort, opportunity, and leisure activity were associated with exercise. In conclusion, it is necessary to educate older persons with disability about a true meaning of physical activity and providing more physical activity opportunities and decreasing inconvenience should be systematically structured in Korea. PMID:27656637

Revenues and Expenditures for Public Elementary and Secondary Education: School Year 2006-07 (Fiscal Year 2007): First Look. NCES 2009-337

ERIC Educational Resources Information Center

Zhou, Lei

2009-01-01

This report presents findings on public education revenues and expenditures using fiscal year 2007 (FY 07) data from the National Public Education Financial Survey (NPEFS) of the Common Core of Data (CCD) survey system. Programs covered in the NPEFS include regular, special, and vocational education; charter schools that reported data to the state…

Magnetic Field of Conductive Objects as Superposition of Elementary Eddy Currents and Eddy Current Tomography

NASA Astrophysics Data System (ADS)

Sukhanov, D. Ya.; Zav'yalova, K. V.

2018-03-01

The paper represents induced currents in an electrically conductive object as a totality of elementary eddy currents. The proposed scanning method includes measurements of only one component of the secondary magnetic field. Reconstruction of the current distribution is performed by deconvolution with regularization. Numerical modeling supported by the field experiments show that this approach is of direct practical relevance.

The Cassette Tape Recorder Means Versus Written and Symbolic Means of Providing Feedback of a Student's Performance on Secondary School Science Laboratory Exercises.

ERIC Educational Resources Information Center

Tauber, Robert T.; Fowler, H. Seymour

Reported is a study of the relationship between student's performance scores and teacher's means of providing evaluative feedback. The sample included 12 classes of 224 students from the tenth through the twelfth grades. The classes included the disciplines of biology, chemistry, and physics including regular, advanced, traditional, PSSC, and…

Overview of Public Elementary and Secondary Schools and Districts: School Year 1996-97. Statistics in Brief.

ERIC Educational Resources Information Center

National Center for Education Statistics (ED), Washington, DC.

In the 1996-97 school year, 86,058 public schools provided instruction to 45.6 million students in the United States. A statistical overview offers a profile of these schools and students. The majority of public school students, 98.2 percent, were enrolled in regular schools; 0.05 percent were in special education schools; 0.04 percent in…

The Benefit of Being a Big Fish in a Big Pond: Contrast and Assimilation Effects on Academic Self-Concept

ERIC Educational Resources Information Center

Preckel, Franzis; Brull, Matthias

2010-01-01

This study investigates the effects of class-average ability (intelligence) and class type (gifted vs. regular) on Math academic self-concept. The sample comprised 722 fifth-grade students (376 female) in a setting of full-time ability grouping at the top track of the German secondary high school system. Students came from 34 different classes at…

The Prevalence and Correlates of Compassion Fatigue, Compassion Satisfaction, and Burnout among Teachers Working in High-Poverty Urban Public Schools

ERIC Educational Resources Information Center

Abraham-Cook, Shannon

2012-01-01

Although public school educators employed in high-poverty urban districts are likely to encounter traumatized children on a regular basis, there is a scarcity of research exploring the psychological effects of secondary traumatic stress exposure in this population. As such, a primary goal of the study was to explore the prevalence and correlates…

Soil and substrate morphology as witnesses of present and former agricultural landscape management

NASA Astrophysics Data System (ADS)

Chartin, C.; Salvador-Blanes, S.; Hinschberger, F.; Bourennane, H.; Macaire, J.-J.

2009-04-01

Water and tillage erosion, combined with the effect of successive regrouping of the land campaigns, have sensibly modified the morphology of cultivated hillslopes. Nowadays, we can still observe over cultivated landscapes various anthropogenic structures (e.g. lynchets) that correspond to former and/or present field limits. The aim of this work is to spatially characterise the geometry of these various structures, and to assess their relation with soil variability. The 10 ha studied site corresponds to an hillslope located in a small calcareous watershed near Tours in the Parisian Basin (France). Soils are mainly Cambisols (calcaric), Epileptic cambisols (calcaric) and Colluvic cambisols. This watershed is characterised by the presence of many soil accumulation structures and has been submitted to an important regrouping of the lands since the 1960's. The existing structures were accurately located and defined through a topographical analysis (slope, profile curvature...), and then related to past and present field limits using aerial photographies and cadastral maps. Two main morphological structures, deeply marked in the topography, are identified. The most remarkable type corresponds to well developed lynchets located at the lower part of field limits. Secondary structures, less marked than lynchets, are linked to field limits which existed at least since 1836, but that disappeared from the 1960's. These secondary structures look like longitudinal bulges placed perpendicularly to the direction of the main slope. A soil survey on these two geomorphic structure types has been performed in order to determine their specific geometry. Lynchets are characterised by a large increase in the thickness of soils: from 35 cm at 24 m upslope to more than 120 cm on its top. But, in some cases, the elevation study shows a topographical discontinuity between the top of the accumulation and the field or road below, discontinuity that is more important than the maximum soil thickness observed in the lynchet. This implies that the substrate, which is mostly homogeneous, has been largely excavated below these limits certainly due to repeated tillage operations. Concerning the secondary structures, soil thickness increases slightly from 35 cm at 16 m up- and downslope the former field limit to 70 cm at the maximum of the bulges convexity. However, the slope morphology seems to show larger soil accumulation considering a regular substrate morphology along the hillslope profile. Here too, by combining soil thickness and surface topography, we show that the substrate has certainly been strongly remodelled at these former field limits by tillage erosion. The spatial variability of the various soils types is closely linked to the sequence of structures oriented perpendicularly to the direction of the main slope. Although the current topography is clearly marked by various structures linked to former and present field limits, it appears that soil thickness is not the only factor explaining these large variations in the slope morphology: long-term agricultural practices, certainly tillage, "shape" the substrate as well. It is thus important to take into account these substrate excavations for sediment budget studies. The use of tracers such as 137Cs will allow to understand the intensity of these morphological changes at the slope scale within the last decades.

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

[Anatomy and histology of salivary glands of Triatominae].

PubMed

Lacombe, D

1999-01-01

Histological studies upon the salivary glands of ten species of triatomine bugs were performed looking for their number and structural organization in different genera. It was possible to evaluate the celular epithelium type of each gland, as well as the merocrine and apocrine secretions of the glands. Secretion run until the hilo and after to salivary pump and hypofaringe. The glandular components, D1, D2 and D3 are always present in the Triatoma, Panstrongylus and Diptelogaster but in Rhodnius there are only the first two pairs of glands. The salivary channels and the hilo are analyzed by histology. The whole pair D3 has a clear valve that regularizes the exit of the secretions to the hilo. According to the genus the valves appear in different locations. They have low and dense epithelium, and their nucleus are rich in chromatin. The secondary channels leaving these valves, are very different, with clear chitinous ringer, low level of chromatin in the nucleus and homogeneous cytoplasm.

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.

Ontogenetic tissue modification in Malus fruit peduncles: the role of sclereids

PubMed Central

Horbens, Melanie; Feldner, Alexander; Höfer, Monika; Neinhuis, Christoph

2014-01-01

Background and Aims Apple (Malus) fruit peduncles are highly modified stems with limited secondary growth because fruit ripening lasts only one season. They must reliably connect rather heavy fruits to the branch and cope with increasing fruit weight, which induces dynamic stresses under oscillating wind loads. This study focuses on tissue modification of these small, exposed structures during fruit development. Methods A combination of microscopic, static and dynamic mechanical tests, as well as Raman spectroscopy, was used to study structure–function relationships in peduncles of one cultivar and 12 wild species, representatively chosen from all sections of the genus Malus. Tissue differentiation and ontogenetic changes in mechanical properties of Malus peduncles were observed throughout one growing season and after successive removal of tissues. Key Results Unlike in regular stems, the vascular cambium produces mainly phloem during secondary growth. Hence, in addition to a reduced xylem, all species developed a centrally arranged sclerenchyma ring composed of fibres and brachysclereids. Based on differences in cell-wall thickness, and proportions and arrangement of sclereids, two types of peduncle construction could be distinguished. Fibres provide an increased maximum tensile strength and contribute most to the overall axial rigidity of the peduncles. Sclereids contribute insignificantly to peduncle strength; however, despite being shown to have a lower elastic modulus than fibres, they are the most effective tissue in stiffening peduncles against bending. Conclusions The experimental data revealed that sclereids originating from cortical parenchyma act as ‘accessory’ cells to enhance proportions of sclerenchyma during secondary growth in peduncles. The mechanism can be interpreted as an adaptation to continuously increasing fruit loads. Under oscillating longitudinal stresses, sclereids may be regarded as regulating elements between maintenance of stiffness and viscous damping, the latter property being attributed to the cortical parenchyma. PMID:24287811

Local Structural Differences in Homologous Proteins: Specificities in Different SCOP Classes

PubMed Central

Joseph, Agnel Praveen; Valadié, Hélène; Srinivasan, Narayanaswamy; de Brevern, Alexandre G.

2012-01-01

The constant increase in the number of solved protein structures is of great help in understanding the basic principles behind protein folding and evolution. 3-D structural knowledge is valuable in designing and developing methods for comparison, modelling and prediction of protein structures. These approaches for structure analysis can be directly implicated in studying protein function and for drug design. The backbone of a protein structure favours certain local conformations which include α-helices, β-strands and turns. Libraries of limited number of local conformations (Structural Alphabets) were developed in the past to obtain a useful categorization of backbone conformation. Protein Block (PB) is one such Structural Alphabet that gave a reasonable structure approximation of 0.42 Å. In this study, we use PB description of local structures to analyse conformations that are preferred sites for structural variations and insertions, among group of related folds. This knowledge can be utilized in improving tools for structure comparison that work by analysing local structure similarities. Conformational differences between homologous proteins are known to occur often in the regions comprising turns and loops. Interestingly, these differences are found to have specific preferences depending upon the structural classes of proteins. Such class-specific preferences are mainly seen in the all-β class with changes involving short helical conformations and hairpin turns. A test carried out on a benchmark dataset also indicates that the use of knowledge on the class specific variations can improve the performance of a PB based structure comparison approach. The preference for the indel sites also seem to be confined to a few backbone conformations involving β-turns and helix C-caps. These are mainly associated with short loops joining the regular secondary structures that mediate a reversal in the chain direction. Rare β-turns of type I’ and II’ are also identified as preferred sites for insertions. PMID:22745680

Periodic surface structure creation by UV femtosecond pulses on silicon

NASA Astrophysics Data System (ADS)

Gilicze, Barnabás; Moczok, Márió; Madarász, Dániel; Juhász, Nóra; Racskó, Bence; Nánai, László

2017-01-01

Laser-induced periodic surface structures are created on Si (100) and Si (111) wafers by 500 fs laser pulses at 248 nm. The periodic structure is concentric and highly regular. The spatial period is consistently varying between 1.1 µm and 3.3 µm in the radial direction. It is shown that the fluence of the irradiation at the same pulse number determines the size of the area where the periodic structure is created and for the same fluence the pulse number determines the regularity of the created grooves by melting processes. The origin of this structure is identified as the inhomogeneity of the laser beam profile caused by Fresnel diffraction close to the focal plane. Further improvement of the formation of periodic structure with femtosecond laser pulses is suggested.

Wave drift damping acting on multiple circular cylinders (model tests)

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

Kinoshita, Takeshi; Sunahara, Shunji; Bao, W.

1995-12-31

The wave drift damping for the slow drift motion of a four-column platform is experimentally investigated. The estimation of damping force of the slow drift motion of moored floating structures in ocean waves, is one of the most important topics. Bao et al. calculated an interaction of multiple circular cylinders based on the potential flow theory, and showed that the wave drift damping is significantly influenced by the interaction between cylinders. This calculation method assumes that the slow drift motion is approximately replaced by steady current, that is, structures on slow drift motion are supposed to be equivalent to onesmore » in both regular waves and slow current. To validate semi-analytical solutions of Bao et al., experiments were carried out. At first, added resistance due to waves acting on a structure composed of multiple (four) vertical circular cylinders fixed to a slowly moving carriage, was measured in regular waves. Next, the added resistance of the structure moored by linear spring to the slowly moving carriage were measured in regular waves. Furthermore, to validate the assumption that the slow drift motion is replaced by steady current, free decay tests in still water and in regular waves were compared with the simulation of the slow drift motion using the wave drift damping coefficient obtained by the added resistance tests.« less

[Perineal urethrostomy plus secondary urethroplasty for ultralong urethral stricture: clinical outcomes and influence on the patient's quality of life].

PubMed

Wang, Yong-Quan; Zhang, Heng; Shen, Wen-Hao; Li, Long-Kun; Li, Wei-Bing; Xiong, En-Qing

2012-04-01

To investigate the outcomes of perineal urethrostomy plus secondary urethroplasty for ultralong urethral stricture and assess its influence on the patient's quality of life. We retrospectively analyzed 54 cases of ultralong urethral stricture treated by perineal urethrostomy from 2000 to 2010. The mean age of the patients was 40 years, and the average length of stricture was 6.5 cm. We evaluated the patients'quality of life by questionnaire investigation and the clinical outcomes based on IPSS, Qmax, the necessity of urethral dilation and satisfaction of the patients. The mean Qmax of the 54 patients was (14.0 +/- 4.7) ml/min. Of the 34 cases that underwent secondary urethroplasty, 22 (64.7%) achieved a mean Qmax of (12.0 +/- 3.5) ml/min, 8 (23.5%) needed regular urethral dilatation and 4 (11.8%) received internal urethrotomy because of restenosis. IPSS scores were 5.4 +/- 2.1 and 8.5 +/- 5.8 after perineal urethrostomy and secondary urethroplasty, respectively. Fifty of the total number of patients (92.6%) were satisfied with the results of perineal urethrostomy, and 22 of the 34 (64.7%) with the results of secondary urethroplasty. Perineal urethrostomy plus secondary urethroplasty is safe and effective for ultralong urethral stricture, and affects very little the patient's quality of life.

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/.

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

Brain Imaging Studies on the Cognitive, Pharmacological and Neurobiological Effects of Cannabis in Humans: Evidence from Studies of Adult Users.

PubMed

Weinstein, Aviv; Livny, Abigail; Weizman, Abraham

2016-01-01

Cannabis is the most widely used illicit drug worldwide. Regular cannabis use has been associated with a range of acute and chronic mental health problems, such as anxiety, depression, psychotic symptoms and neurocognitive impairments and their neural mechanisms need to be examined. This review summarizes and critically evaluates brain-imaging studies of cannabis in recreational and regular cannabis users between January 2000 and January 2016. The search has yielded eligible 103 structural and functional studies. Regular use of cannabis results in volumetric, gray matter and white matter structural changes in the brain, in particular in the hippocampus and the amygdala. Regular use of cannabis affects cognitive processes such as attention, memory, inhibitory control, decision-making, emotional processing, social cognition and their associated brain areas. There is evidence that regular cannabis use leads to altered neural function during attention and working memory and that recruitment of activity in additional brain regions can compensate for it. Similar to other drugs of abuse, cannabis cues activated areas in the reward pathway. Pharmacological studies showed a modest increase in human striatal dopamine transmission after administration of THC in healthy volunteers. Regular cannabis use resulted in reduced dopamine transporter occupancy and reduced dopamine synthesis but not in reduced striatal D2/D3 receptor occupancy compared with healthy control participants. Studies also showed different effects of Δ-9 tetrahydrocannabinol (THC) and cannabidiol (CBD) on emotion, cognition and associated brain regions in healthy volunteers, whereby CBD protects against the psychoactive effects of THC. Brain imaging studies using selective high-affinity radioligands for the imaging of cannabinoid CB1 receptor availability in Positron Emission Tomography (PET) showed downregulation of CB1 in regular users of cannabis. In conclusion, regular use of the cannabinoids exerts structural and functional changes in the human brain. These changes have profound implications for our understanding of the neuropharmacology of cannabis and its effects on cognition, mental health and the brain. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

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…

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/.

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.

Identification of subsurface structures using electromagnetic data and shape priors

NASA Astrophysics Data System (ADS)

Tveit, Svenn; Bakr, Shaaban A.; Lien, Martha; Mannseth, Trond

2015-03-01

We consider the inverse problem of identifying large-scale subsurface structures using the controlled source electromagnetic method. To identify structures in the subsurface where the contrast in electric conductivity can be small, regularization is needed to bias the solution towards preserving structural information. We propose to combine two approaches for regularization of the inverse problem. In the first approach we utilize a model-based, reduced, composite representation of the electric conductivity that is highly flexible, even for a moderate number of degrees of freedom. With a low number of parameters, the inverse problem is efficiently solved using a standard, second-order gradient-based optimization algorithm. Further regularization is obtained using structural prior information, available, e.g., from interpreted seismic data. The reduced conductivity representation is suitable for incorporation of structural prior information. Such prior information cannot, however, be accurately modeled with a gaussian distribution. To alleviate this, we incorporate the structural information using shape priors. The shape prior technique requires the choice of kernel function, which is application dependent. We argue for using the conditionally positive definite kernel which is shown to have computational advantages over the commonly applied gaussian kernel for our problem. Numerical experiments on various test cases show that the methodology is able to identify fairly complex subsurface electric conductivity distributions while preserving structural prior information during the inversion.

Complex supramolecular interfacial tessellation through convergent multi-step reaction of a dissymmetric simple organic precursor

NASA Astrophysics Data System (ADS)

Zhang, Yi-Qi; Paszkiewicz, Mateusz; Du, Ping; Zhang, Liding; Lin, Tao; Chen, Zhi; Klyatskaya, Svetlana; Ruben, Mario; Seitsonen, Ari P.; Barth, Johannes V.; Klappenberger, Florian

2018-03-01

Interfacial supramolecular self-assembly represents a powerful tool for constructing regular and quasicrystalline materials. In particular, complex two-dimensional molecular tessellations, such as semi-regular Archimedean tilings with regular polygons, promise unique properties related to their nontrivial structures. However, their formation is challenging, because current methods are largely limited to the direct assembly of precursors, that is, where structure formation relies on molecular interactions without using chemical transformations. Here, we have chosen ethynyl-iodophenanthrene (which features dissymmetry in both geometry and reactivity) as a single starting precursor to generate the rare semi-regular (3.4.6.4) Archimedean tiling with long-range order on an atomically flat substrate through a multi-step reaction. Intriguingly, the individual chemical transformations converge to form a symmetric alkynyl-Ag-alkynyl complex as the new tecton in high yields. Using a combination of microscopy and X-ray spectroscopy tools, as well as computational modelling, we show that in situ generated catalytic Ag complexes mediate the tecton conversion.

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.

Regular Topographic Patterning of Karst Depressions Suggests Landscape Self-Organization

NASA Astrophysics Data System (ADS)

Quintero, C.; Cohen, M. J.

2017-12-01

Thousands of wetland depressions that are commonly host to cypress domes dot the sub-tropical limestone landscape of South Florida. The origin of these depression features has been the topic of debate. Here we build upon the work of previous surveyors of this landscape to analyze the morphology and spatial distribution of depressions on the Big Cypress landscape. We took advantage of the emergence and availability of high resolution Light Direction and Ranging (LiDAR) technology and ArcMap GIS software to analyze the structure and regularity of landscape features with methods unavailable to past surveyors. Six 2.25 km2 LiDAR plots within the preserve were selected for remote analysis and one depression feature within each plot was selected for more intensive sediment and water depth surveying. Depression features on the Big Cypress landscape were found to show strong evidence of regular spatial patterning. Periodicity, a feature of regularly patterned landscapes, is apparent in both Variograms and Radial Spectrum Analyses. Size class distributions of the identified features indicate constrained feature sizes while Average Nearest Neighbor analyses support the inference of dispersed features with non-random spacing. The presence of regular patterning on this landscape strongly implies biotic reinforcement of spatial structure by way of the scale dependent feedback. In characterizing the structure of this wetland landscape we add to the growing body of work dedicated to documenting how water, life and geology may interact to shape the natural landscapes we see today.

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.

A comparative molecular dynamics study of thermophilic and mesophilic β-fructosidase enzymes.

PubMed

Mazola, Yuliet; Guirola, Osmany; Palomares, Sucel; Chinea, Glay; Menéndez, Carmen; Hernández, Lázaro; Musacchio, Alexis

2015-09-01

Arabidopsis thaliana cell wall invertase 1 (AtcwINV1) and Thermotoga maritima β-fructosidase (BfrA) are among the best structurally studied members of the glycoside hydrolase family 32. Both enzymes hydrolyze sucrose as the main substrate but differ strongly in their thermal stability. Mesophilic AtcwINV1 and thermophilic BfrA have divergent sequence similarities in the N-terminal five bladed β-propeller catalytic domain (31 %) and the C-terminal β-sandwich domain (15 %) of unknown function. The two enzymes were subjected to 200 ns molecular dynamics simulations at 300 K (27 °C) and 353 K (80 °C). Regular secondary structure regions, but not loops, in AtcwINV1 and BfrA showed no significant fluctuation differences at both temperatures. BfrA was more rigid than AtcwINV1 at 300 K. The simulation at 353 K did not alter the structural stability of BfrA, but did increase the overall flexibility of AtcwINV1 exhibiting the most fluctuating regions in the β-propeller domain. The simulated heat treatment also increased the gyration radius and hydrophobic solvent accessible surface area of the plant enzyme, consistent with the initial steps of an unfolding process. The preservation of the conformational rigidity of BfrA at 353 K is linked to the shorter size of the protein loops. Shortening of BfrA loops appears to be a key mechanism for thermostability.

Transcranial direct current stimulation in post-stroke sub-acute aphasia: study protocol for a randomized controlled trial.

PubMed

Spielmann, Kerstin; van de Sandt-Koenderman, W Mieke E; Heijenbrok-Kal, Majanka H; Ribbers, Gerard M

2016-08-02

Transcranial direct current stimulation (tDCS) is a promising new technique to optimize the effect of regular Speech and Language Therapy (SLT) in the context of aphasia rehabilitation. The present study focuses on the effect of tDCS provided during SLT in the sub-acute stage after stroke. The primary aim is to evaluate the potential effect of tDCS on language functioning, specifically on word-finding, as well as generalization effects to verbal communication. The secondary aim is to evaluate its effect on social participation and quality of life, and its cost-effectiveness. We strive to include 58 stroke patients with aphasia, enrolled in an inpatient or outpatient stroke rehabilitation program, in a multicenter, double-blind, randomized controlled trial with two parallel groups and 6 months' follow-up. Patients will participate in two separate intervention weeks, with a pause of 2 weeks in between, in the context of their regular aphasia rehabilitation program. The two intervention weeks comprise daily 45-minute sessions of word-finding therapy, combined with either anodal tDCS over the left inferior frontal gyrus (1 mA, 20 minutes; experimental condition) or sham-tDCS over the same region (control condition). The primary outcome measure is word-finding. Secondary outcome measures are verbal communication, social participation, quality of life, and cost-effectiveness of the intervention. Our results will contribute to the discussion on whether tDCS should be implemented in regular aphasia rehabilitation programs for the sub-acute post-stroke population in terms of (cost-)effectiveness. Nederlands Trail Register: NTR4364 . Registered on 21 February 2014.

Depression and smoking characteristics among HIV-positive smokers in Russia: A cross-sectional study.

PubMed

Lasser, Karen E; Lunze, Karsten; Cheng, Debbie M; Blokhina, Elena; Walley, Alexander Y; Tindle, Hilary A; Quinn, Emily; Gnatienko, Natalia; Krupitsky, Evgeny; Samet, Jeffrey H

2018-01-01

Globally, persons with HIV infection, depression and substance use disorders have a higher smoking prevalence and smoke more heavily than other populations. These associations have not been explored among Russian smokers with HIV infection and substance use disorders. The purpose of this study was to examine the relationship between the presence of depressive symptoms and smoking outcomes in an HIV-positive cohort of Russian smokers with a history of substance use disorders (alcohol and/or drug use disorders). We performed a cross-sectional secondary data analysis of a cohort of HIV-positive regular smokers with a history of substance use disorders recruited in St. Petersburg, Russia in 2012-2015. The primary outcome was heavy smoking, defined as smoking > 20 cigarettes per day. Nicotine dependence (moderate-very high) was a secondary outcome. The main independent variable was a high level of depressive symptoms in the past 7 days (defined as CES-D > = 24). We used multivariable logistic regression to examine associations between depressive symptoms and the outcomes, controlling for age, sex, education, income, running out of money for housing/food, injection drug use, and alcohol use measured by the AUDIT. Among 309 regular smokers, 79 participants (25.6%) had high levels of depressive symptoms, and 65 participants (21.0%) were heavy smokers. High levels of depressive symptoms were not significantly associated with heavy smoking (adjusted odds ratio [aOR] 1.50, 95% CI 0.78-2.89) or with moderate-very high levels of nicotine dependence (aOR 1.35, 95% CI 0.75-2.41). This study did not detect an association between depressive symptoms and smoking outcomes among HIV-positive regular smokers in Russia.

Assessment of Primary Health Care in the Treatment of Tuberculosis in a Brazilian Locality of the International Triple Frontier

PubMed Central

Silva-Sobrinho, Reinaldo Antonio; Wysocki, Anneliese Domingues; Scatena, Lúcia Marina; Pinto, Erika Simone Galvão; Beraldo, Aline Ale; Andrade, Rubia Laine Paula; Zilly, Adriana; Munhak da Silva, Rosane Meire; Gomes, Michela Prestes; Mayer, Paulo César Morales; Ruffino-Netto, Antonio; Villa, Tereza Cristina Scatena

2017-01-01

Objective: To evaluate the performance of Primary Health Care (PHC) in treatment of TB patients in a triple international border municipality. Methods: The present study was an evaluative survey of cross-sectional and quantitative approach conducted with 225 PHC healthcare professionals. Data was collected through a structured and validated instrument, which provided five indicators of "structure" and four indicators of "process" classified as unsatisfactory, regular or satisfactory. Results: The "structure" component was unsatisfactory for the indicator of professionals involved in TB care and training, and regular for the indicator of connection between the units and other levels of care. The "process" component was regular for the indicators of TB information, directly observed treatment and reference and counter reference on TB, and unsatisfactory for external actions on TB control. Conclusion: The "structure" and "process" components points out some weaknesses in terms of management and organization of human resources. Low frequency of training and the turnover influenced the involvement of professionals. Elements of "structure" and "process" show the need for investing in the PHC team and improving the clinical management of cases. PMID:29204229

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.

Effect of von Karman Vortex Shedding on Regular and Open-slit V-gutter Stabilized Turbulent Premixed Flames

DTIC Science & Technology

2012-04-01

Both flame lengths shrink and large scale disruptions occur downstream with vortex shedding carrying reaction zones. Flames in both flameholders...9) the flame structure changes dramatically for both regular and open-slit V-gutter. Both flame lengths shrink and large scale disruptions occur...reduces the flame length . However, qualitatively the open-slit V-gutter appears to be more sensitive than the regular V-gutter. Both flames remain

[Clustered regularly interspaced short palindromic repeats: structure, function and application--a review].

PubMed

Cui, Yujun; Li, Yanjun; Yan, Yanfeng; Yang, Ruifu

2008-11-01

CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats), the basis of spoligotyping technology, can provide prokaryotes with heritable adaptive immunity against phages' invasion. Studies on CRISPR loci and their associated elements, including various CAS (CRISPR-associated) proteins and leader sequences, are still in its infant period. We introduce the brief history', structure, function, bioinformatics research and application of this amazing immunity system in prokaryotic organism for inspiring more scientists to find their interest in this developing topic.

Physical activity in primary and secondary prevention of cardiovascular disease: Overview updated.

PubMed

Alves, Alberto J; Viana, João L; Cavalcante, Suiane L; Oliveira, Nórton L; Duarte, José A; Mota, Jorge; Oliveira, José; Ribeiro, Fernando

2016-10-26

Although the observed progress in the cardiovascular disease treatment, the incidence of new and recurrent coronary artery disease remains elevated and constitutes the leading cause of death in the developed countries. Three-quarters of deaths due to cardiovascular diseases could be prevented with adequate changes in lifestyle, including increased daily physical activity. New evidence confirms that there is an inverse dose-response relationship between physical activity and cardiovascular disease and mortality risk. However, participation in moderate to vigorous physical activity may not fully attenuate the independent effect of sedentary activities on increased risk for cardiovascular diseases. Physical activity also plays an important role in secondary prevention of cardiovascular diseases by reducing the impact of the disease, slowing its progress and preventing recurrence. Nonetheless, most of eligible cardiovascular patients still do not benefit from secondary prevention/cardiac rehabilitation programs. The present review draws attention to the importance of physical activity in the primary and secondary prevention of cardiovascular diseases. It also addresses the mechanisms by which physical activity and regular exercise can improve cardiovascular health and reduce the burden of the disease.

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.

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.

Space Weather Effects on Range Operations

DTIC Science & Technology

2013-02-01

to give a significant albedo neutron flux at LEO spacecraft. The decay of these albedo neutrons into protons is believed to populate the inner...significant fluxes of secondary neutrons . This mechanism is thought to be the dominant SEE hazard for current and near future avionics at most... neutron monitor at Climax. A version of the CREAM detector made regular flights on-board Concorde G-BOAB between November 1988 and December 1992. Results

Secondary Breast Augmentation: Managing Each Case

PubMed Central

Sanchez, Kyrenia

2010-01-01

Breast augmentation is one of the most regularly performed interventions requiring reoperation in aesthetic surgery. For this reason, it involves a greater chance for complications. In this report, the authors aim to provide young plastic surgeons with guidelines based on their experience for responding to each of these complications, to explain the causes and ways of avoiding them, and to show how they can be treated when they occur. PMID:20838791

The Relationship between Class Attitudes towards Peers with a Disability and Peer Acceptance, Friendships and Peer Interactions of Students with a Disability in Regular Secondary Schools

ERIC Educational Resources Information Center

Petry, Katja

2018-01-01

Students with a disability in inclusive classes often face problems with peer acceptance, friendships and peer interactions. In this paper, the relationship between these difficulties in social participation and the attitudes that typically developing adolescents hold towards peers with a disability at the level of the class was explored. A…

Dynamics of coherent states in regular and chaotic regimes of the non-integrable Dicke model

NASA Astrophysics Data System (ADS)

Lerma-Hernández, S.; Chávez-Carlos, J.; Bastarrachea-Magnani, M. A.; López-del-Carpio, B.; Hirsch, J. G.

2018-04-01

The quantum dynamics of initial coherent states is studied in the Dicke model and correlated with the dynamics, regular or chaotic, of their classical limit. Analytical expressions for the survival probability, i.e. the probability of finding the system in its initial state at time t, are provided in the regular regions of the model. The results for regular regimes are compared with those of the chaotic ones. It is found that initial coherent states in regular regions have a much longer equilibration time than those located in chaotic regions. The properties of the distributions for the initial coherent states in the Hamiltonian eigenbasis are also studied. It is found that for regular states the components with no negligible contribution are organized in sequences of energy levels distributed according to Gaussian functions. In the case of chaotic coherent states, the energy components do not have a simple structure and the number of participating energy levels is larger than in the regular cases.

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.

A space-frequency multiplicative regularization for force reconstruction problems

NASA Astrophysics Data System (ADS)

Aucejo, M.; De Smet, O.

2018-05-01

Dynamic forces reconstruction from vibration data is an ill-posed inverse problem. A standard approach to stabilize the reconstruction consists in using some prior information on the quantities to identify. This is generally done by including in the formulation of the inverse problem a regularization term as an additive or a multiplicative constraint. In the present article, a space-frequency multiplicative regularization is developed to identify mechanical forces acting on a structure. The proposed regularization strategy takes advantage of one's prior knowledge of the nature and the location of excitation sources, as well as that of their spectral contents. Furthermore, it has the merit to be free from the preliminary definition of any regularization parameter. The validity of the proposed regularization procedure is assessed numerically and experimentally. It is more particularly pointed out that properly exploiting the space-frequency characteristics of the excitation field to identify can improve the quality of the force reconstruction.

Structured sparse linear graph embedding.

PubMed

Wang, Haixian

2012-03-01

Subspace learning is a core issue in pattern recognition and machine learning. Linear graph embedding (LGE) is a general framework for subspace learning. In this paper, we propose a structured sparse extension to LGE (SSLGE) by introducing a structured sparsity-inducing norm into LGE. Specifically, SSLGE casts the projection bases learning into a regression-type optimization problem, and then the structured sparsity regularization is applied to the regression coefficients. The regularization selects a subset of features and meanwhile encodes high-order information reflecting a priori structure information of the data. The SSLGE technique provides a unified framework for discovering structured sparse subspace. Computationally, by using a variational equality and the Procrustes transformation, SSLGE is efficiently solved with closed-form updates. Experimental results on face image show the effectiveness of the proposed method. Copyright © 2011 Elsevier Ltd. All rights reserved.

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.

Structure-Function Network Mapping and Its Assessment via Persistent Homology

PubMed Central

2017-01-01

Understanding the relationship between brain structure and function is a fundamental problem in network neuroscience. This work deals with the general method of structure-function mapping at the whole-brain level. We formulate the problem as a topological mapping of structure-function connectivity via matrix function, and find a stable solution by exploiting a regularization procedure to cope with large matrices. We introduce a novel measure of network similarity based on persistent homology for assessing the quality of the network mapping, which enables a detailed comparison of network topological changes across all possible thresholds, rather than just at a single, arbitrary threshold that may not be optimal. We demonstrate that our approach can uncover the direct and indirect structural paths for predicting functional connectivity, and our network similarity measure outperforms other currently available methods. We systematically validate our approach with (1) a comparison of regularized vs. non-regularized procedures, (2) a null model of the degree-preserving random rewired structural matrix, (3) different network types (binary vs. weighted matrices), and (4) different brain parcellation schemes (low vs. high resolutions). Finally, we evaluate the scalability of our method with relatively large matrices (2514x2514) of structural and functional connectivity obtained from 12 healthy human subjects measured non-invasively while at rest. Our results reveal a nonlinear structure-function relationship, suggesting that the resting-state functional connectivity depends on direct structural connections, as well as relatively parsimonious indirect connections via polysynaptic pathways. PMID:28046127

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

Field-induced assembly of colloidal ellipsoids into well-defined microtubules

PubMed Central

Crassous, Jérôme J.; Mihut, Adriana M.; Wernersson, Erik; Pfleiderer, Patrick; Vermant, Jan; Linse, Per; Schurtenberger, Peter

2014-01-01

Current theoretical attempts to understand the reversible formation of stable microtubules and virus shells are generally based on shape-specific building blocks or monomers, where the local curvature of the resulting structure is explicitly built-in via the monomer geometry. Here we demonstrate that even simple ellipsoidal colloids can reversibly self-assemble into regular tubular structures when subjected to an alternating electric field. Supported by model calculations, we discuss the combined effects of anisotropic shape and field-induced dipolar interactions on the reversible formation of self-assembled structures. Our observations show that the formation of tubular structures through self-assembly requires much less geometrical and interaction specificity than previously thought, and advance our current understanding of the minimal requirements for self-assembly into regular virus-like structures. PMID:25409686

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.

Group-sparse representation with dictionary learning for medical image denoising and fusion.

PubMed

Li, Shutao; Yin, Haitao; Fang, Leyuan

2012-12-01

Recently, sparse representation has attracted a lot of interest in various areas. However, the standard sparse representation does not consider the intrinsic structure, i.e., the nonzero elements occur in clusters, called group sparsity. Furthermore, there is no dictionary learning method for group sparse representation considering the geometrical structure of space spanned by atoms. In this paper, we propose a novel dictionary learning method, called Dictionary Learning with Group Sparsity and Graph Regularization (DL-GSGR). First, the geometrical structure of atoms is modeled as the graph regularization. Then, combining group sparsity and graph regularization, the DL-GSGR is presented, which is solved by alternating the group sparse coding and dictionary updating. In this way, the group coherence of learned dictionary can be enforced small enough such that any signal can be group sparse coded effectively. Finally, group sparse representation with DL-GSGR is applied to 3-D medical image denoising and image fusion. Specifically, in 3-D medical image denoising, a 3-D processing mechanism (using the similarity among nearby slices) and temporal regularization (to perverse the correlations across nearby slices) are exploited. The experimental results on 3-D image denoising and image fusion demonstrate the superiority of our proposed denoising and fusion approaches.

Convex blind image deconvolution with inverse filtering

NASA Astrophysics Data System (ADS)

Lv, Xiao-Guang; Li, Fang; Zeng, Tieyong

2018-03-01

Blind image deconvolution is the process of estimating both the original image and the blur kernel from the degraded image with only partial or no information about degradation and the imaging system. It is a bilinear ill-posed inverse problem corresponding to the direct problem of convolution. Regularization methods are used to handle the ill-posedness of blind deconvolution and get meaningful solutions. In this paper, we investigate a convex regularized inverse filtering method for blind deconvolution of images. We assume that the support region of the blur object is known, as has been done in a few existing works. By studying the inverse filters of signal and image restoration problems, we observe the oscillation structure of the inverse filters. Inspired by the oscillation structure of the inverse filters, we propose to use the star norm to regularize the inverse filter. Meanwhile, we use the total variation to regularize the resulting image obtained by convolving the inverse filter with the degraded image. The proposed minimization model is shown to be convex. We employ the first-order primal-dual method for the solution of the proposed minimization model. Numerical examples for blind image restoration are given to show that the proposed method outperforms some existing methods in terms of peak signal-to-noise ratio (PSNR), structural similarity (SSIM), visual quality and time consumption.

Iterative image reconstruction for multienergy computed tomography via structure tensor total variation regularization

NASA Astrophysics Data System (ADS)

Zeng, Dong; Bian, Zhaoying; Gong, Changfei; Huang, Jing; He, Ji; Zhang, Hua; Lu, Lijun; Feng, Qianjin; Liang, Zhengrong; Ma, Jianhua

2016-03-01

Multienergy computed tomography (MECT) has the potential to simultaneously offer multiple sets of energy- selective data belonging to specific energy windows. However, because sufficient photon counts are not available in the specific energy windows compared with that in the whole energy window, the MECT images reconstructed by the analytical approach often suffer from poor signal-to-noise (SNR) and strong streak artifacts. To eliminate this drawback, in this work we present a penalized weighted least-squares (PWLS) scheme by incorporating the new concept of structure tensor total variation (STV) regularization to improve the MECT images quality from low-milliampere-seconds (low-mAs) data acquisitions. Henceforth the present scheme is referred to as `PWLS- STV' for simplicity. Specifically, the STV regularization is derived by penalizing the eigenvalues of the structure tensor of every point in the MECT images. Thus it can provide more robust measures of image variation, which can eliminate the patchy artifacts often observed in total variation regularization. Subsequently, an alternating optimization algorithm was adopted to minimize the objective function. Experiments with a digital XCAT phantom clearly demonstrate that the present PWLS-STV algorithm can achieve more gains than the existing TV-based algorithms and the conventional filtered backpeojection (FBP) algorithm in terms of noise-induced artifacts suppression, resolution preservation, and material decomposition assessment.

Crystallography of rare galactic honeycomb structure near supernova 1987a

NASA Technical Reports Server (NTRS)

Noever, David A.

1994-01-01

Near supernova 1987a, the rare honeycomb structure of 20-30 galactic bubbles measures 30 x 90 light years. Its remarkable regularity in bubble size suggests a single-event origin which may correlate with the nearby supernova. To test the honeycomb's regularity in shape and size, the formalism of statistical crystallography is developed here for bubble sideness. The standard size-shape relations (Lewis's law, Desch's law, and Aboav-Weaire's law) govern area, perimeter and nearest neighbor shapes. Taken together, they predict a highly non-equilibrium structure for the galactic honeycomb which evolves as a bimodal shape distribution without dominant bubble perimeter energy.

Boosting Maintenance in Working Memory with Temporal Regularities

ERIC Educational Resources Information Center

Plancher, Gaën; Lévêque, Yohana; Fanuel, Lison; Piquandet, Gaëlle; Tillmann, Barbara

2018-01-01

Music cognition research has provided evidence for the benefit of temporally regular structures guiding attention over time. The present study investigated whether maintenance in working memory can benefit from an isochronous rhythm. Participants were asked to remember series of 6 letters for serial recall. In the rhythm condition of Experiment…

Regularization in Short-Term Memory for Serial Order

ERIC Educational Resources Information Center

Botvinick, Matthew; Bylsma, Lauren M.

2005-01-01

Previous research has shown that short-term memory for serial order can be influenced by background knowledge concerning regularities of sequential structure. Specifically, it has been shown that recall is superior for sequences that fit well with familiar sequencing constraints. The authors report a corresponding effect pertaining to serial…

An ecological mechanism to create regular patterns of surface dissolution in a low-relief carbonate landscape

NASA Astrophysics Data System (ADS)

Cohen, M. J.; Martin, J. B.; Mclaughlin, D. L.; Osborne, T.; Murray, A.; Watts, A. C.; Watts, D.; Heffernan, J. B.

2012-12-01

Development of karst landscapes is controlled by focused delivery of water undersaturated with respect to the soluble rock minerals. As that water comes to equilibrium with the rock, secondary porosity is incrementally reinforced creating a positive feedback that acts to augment the drainage network and subsequent water delivery. In most self-organizing systems, spatial positive feedbacks create features (in landscapes: patches; in karst aquifers: conduits) whose size-frequency relationship follows a power function, indicating a higher probability of large features than would occur with a random or Gaussian genesis process. Power functions describe several aspects of secondary porosity in the Upper Floridan Aquifer in north Florida. In contrast, a different pattern arises in the karst landscape in southwest Florida (Big Cypress National Preserve; BICY), where low-relief and a shallow aquiclude govern regional hydrology. There, the landscape pattern is highly regular (Fig. 1), with circular cypress-dominated wetlands occupying depressions that are hydrologically isolated and distributed evenly in a matrix of pine uplands. Regular landscape patterning results from spatially coupled feedbacks, one positive operating locally that expands patches coupled to another negative that operates at distance, eventually inhibiting patch expansion. The positive feedback in BICY is thought to derive from the presence of surface depressions, which sustain prolonged inundation in this low-relief setting, and facilitate wetland development that greatly augments dissolution potential of infiltrating water in response to ecosystem metabolic processes. In short, wetlands "drill" into the carbonate leading to both vertical and lateral basin expansion. Wetland expansion occurs at the expense of surrounding upland area, which is the local catchment that subsidizes water availability. A distal inhibitory feedback on basin expansion thus occurs as the water necessary to sustain prolonged inundation becomes limiting. The implied strong reciprocal coupling between surface production of organic matter and patterns of induced subsurface carbonate dissolution are a novel example of co-evolving biogeomorphic processes in the earth system. Fig. 1 - Regular patterned landscape in Big Cypress National Preserve showing cypress dominated wetlands (round features) embedded in a mosaic of pine and grass uplands. Exposed carbonate rings are evident at the margins of many of the wetland basins.

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.

Single-cycle high-intensity electromagnetic pulse generation in the interaction of a plasma wakefield with regular nonlinear structures.

PubMed

Bulanov, S S; Esirkepov, T Zh; Kamenets, F F; Pegoraro, F

2006-03-01

The interaction of regular nonlinear structures (such as subcycle solitons, electron vortices, and wake Langmuir waves) with a strong wake wave in a collisionless plasma can be exploited in order to produce ultrashort electromagnetic pulses. The electromagnetic field of the nonlinear structure is partially reflected by the electron density modulations of the incident wake wave and a single-cycle high-intensity electromagnetic pulse is formed. Due to the Doppler effect the length of this pulse is much shorter than that of the nonlinear structure. This process is illustrated with two-dimensional particle-in-cell simulations. The considered laser-plasma interaction regimes can be achieved in present day experiments and can be used for plasma diagnostics.

Using Lattice Topology Information to Investigate Persistent Scatterers at Facades in Urban Areas

NASA Astrophysics Data System (ADS)

Schack, L.; Soergel, U.

2013-05-01

Modern spaceborne SAR sensors like TerraSAR-X offer ground resolution of up to one meter in range and azimuth direction. Buildings, roads, bridges, and other man-made structures appear in such data often as regular patterns of strong and temporally stable points (Persistent Scatterer, PS). As one step in the process of unveiling what object structure actually causes the PS (i.e., physical nature) we compare those regular structures in SAR data to their correspondences in optical imagery. We use lattices as a common data representation for visible facades. By exploiting the topology information given by the lattices we can complete gaps in the structures which is one step towards the understanding of the complex scattering characteristics of distinct facade objects.

Effects of Regular and Long-Acting Insulin on Cognition and Alzheimer's Disease Biomarkers: A Pilot Clinical Trial.

PubMed

Craft, Suzanne; Claxton, Amy; Baker, Laura D; Hanson, Angela J; Cholerton, Brenna; Trittschuh, Emily H; Dahl, Deborah; Caulder, Erin; Neth, Bryan; Montine, Thomas J; Jung, Youngkyoo; Maldjian, Joseph; Whitlow, Christopher; Friedman, Seth

2017-01-01

Long acting insulin detemir administered intranasally for three weeks enhanced memory for adults with Alzheimer's disease dementia (AD) or amnestic mild cognitive impairment (MCI). The investigation of longer-term administration is necessary to determine whether benefits persist, whether they are similar to benefits provided by regular insulin, and whether either form of insulin therapy affects AD biomarkers. The present study aimed to determine whether four months of treatment with intranasal insulin detemir or regular insulin improves cognition, daily functioning, and AD biomarkers for adults with MCI or AD. This randomized, double-blind, placebo-controlled trial included an intent-to-treat sample consisting of 36 adults diagnosed with MCI or mild to moderate AD. Participants received placebo (n = 12), 40 IU of insulin detemir (n = 12), or 40 IU of regular insulin (n = 12) daily for four months, administered with a nasal delivery device. A cognitive battery was administered at baseline and after two and four months of treatment. MRI was administered for all participants and lumbar puncture for a subset (n = 20) at baseline and four months. The primary outcome was change from baseline to four months on a memory composite (sum of Z scores for delayed list and story recall). Secondary outcomes included: global cognition (Alzheimer's Disease Assessment Scale-Cognition), daily functioning (Dementia Severity Rating Scale), MRI volume changes in AD-related regions of interest, and cerebrospinal fluid AD markers. The regular insulin treated group had better memory after two and four months compared with placebo (p < 0.03). No significant effects were observed for the detemir-assigned group compared with the placebo group, or for daily functioning for either group. Regular insulin treatment was associated with preserved volume on MRI. Regular insulin treatment was also associated with reduction in the tau-P181/Aβ42 ratio. Future research is warranted to examine the mechanistic basis of treatment differences, and to further assess the efficacy and safety of intranasal insulin.

Computerized tomography with total variation and with shearlets

NASA Astrophysics Data System (ADS)

Garduño, Edgar; Herman, Gabor T.

2017-04-01

To reduce the x-ray dose in computerized tomography (CT), many constrained optimization approaches have been proposed aiming at minimizing a regularizing function that measures a lack of consistency with some prior knowledge about the object that is being imaged, subject to a (predetermined) level of consistency with the detected attenuation of x-rays. One commonly investigated regularizing function is total variation (TV), while other publications advocate the use of some type of multiscale geometric transform in the definition of the regularizing function, a particular recent choice for this is the shearlet transform. Proponents of the shearlet transform in the regularizing function claim that the reconstructions so obtained are better than those produced using TV for texture preservation (but may be worse for noise reduction). In this paper we report results related to this claim. In our reported experiments using simulated CT data collection of the head, reconstructions whose shearlet transform has a small ℓ 1-norm are not more efficacious than reconstructions that have a small TV value. Our experiments for making such comparisons use the recently-developed superiorization methodology for both regularizing functions. Superiorization is an automated procedure for turning an iterative algorithm for producing images that satisfy a primary criterion (such as consistency with the observed measurements) into its superiorized version that will produce results that, according to the primary criterion are as good as those produced by the original algorithm, but in addition are superior to them according to a secondary (regularizing) criterion. The method presented for superiorization involving the ℓ 1-norm of the shearlet transform is novel and is quite general: It can be used for any regularizing function that is defined as the ℓ 1-norm of a transform specified by the application of a matrix. Because in the previous literature the split Bregman algorithm is used for similar purposes, a section is included comparing the results of the superiorization algorithm with the split Bregman algorithm.

The effects of an extensive exercise programme on the progression of Mild Cognitive Impairment (MCI): study protocol for a randomised controlled trial.

PubMed

Devenney, Kate E; Sanders, Marit L; Lawlor, Brian; Olde Rikkert, Marcel G M; Schneider, Stefan

2017-03-22

Exercise interventions to prevent dementia and delay cognitive decline have gained considerable attention in recent years. Human and animal studies have demonstrated that regular physical activity targets brain function by increasing cognitive reserve. There is also evidence of structural changes caused by exercise in preventing or delaying the genesis of neurodegeneration. Although initial studies indicate enhanced cognitive performance in patients with mild cognitive impairment (MCI) following an exercise intervention, little is known about the effect of an extensive, controlled and regular exercise regimen on the neuropathology of patients with MCI. This study aims to determine the effects of an extensive exercise programme on the progression of MCI. This randomised controlled clinical intervention study will take place across three European sites. Seventy-five previously sedentary patients with a clinical diagnosis of MCI will be recruited at each site. Participants will be randomised to one of three groups. One group will receive a standardised 1-year extensive aerobic exercise intervention (3 units of 45 min/week). The second group will complete stretching and toning (non-aerobic) exercise (3 units of 45 min/week) and the third group will act as the control group. Change in all outcomes will be measured at baseline (T0), after six months (T1) and after 12 months (T2). The primary outcome, cognitive performance, will be determined by a neuropsychological test battery (CogState battery, Trail Making Test and Verbal fluency). Secondary outcomes include Montreal Cognitive Assessment (MoCA), cardiovascular fitness, physical activity, structural changes of the brain, quality of life measures and measures of frailty. Furthermore, outcome variables will be related to genetic variations on genes related to neurogenesis and epigenetic changes in these genes caused by the exercise intervention programme. The results will add new insights into the prevailing notion that exercise may slow the rate of cognitive decline in MCI. ClinicalTrials.gov NCT02913053.

Limited Bacterial Diversity within a Treatment Plant Receiving Antibiotic-Containing Waste from Bulk Drug Production.

PubMed

Marathe, Nachiket P; Shetty, Sudarshan A; Shouche, Yogesh S; Larsson, D G Joakim

2016-01-01

Biological treatment of waste water from bulk drug production, contaminated with high levels of fluoroquinolone antibiotics, can lead to massive enrichment of antibiotic resistant bacteria, resistance genes and associated mobile elements, as previously shown. Such strong selection may be boosted by the use of activated sludge (AS) technology, where microbes that are able to thrive on the chemicals within the wastewater are reintroduced at an earlier stage of the process to further enhance degradation of incoming chemicals. The microbial community structure within such a treatment plant is, however, largely unclear. In this study, Illumina-based 16S rRNA amplicon sequencing was applied to investigate the bacterial communities of different stages from an Indian treatment plant operated by Patancheru Environment Technology Limited (PETL) in Hyderabad, India. The plant receives waste water with high levels of fluoroquinolones and applies AS technology. A total of 1,019,400 sequences from samples of different stages of the treatment process were analyzed. In total 202, 303, 732, 652, 947 and 864 operational taxonomic units (OTUs) were obtained at 3% distance cutoff in the equilibrator, aeration tanks 1 and 2, settling tank, secondary sludge and old sludge samples from PETL, respectively. Proteobacteria was the most dominant phyla in all samples with Gammaproteobacteria and Betaproteobacteria being the dominant classes. Alcaligenaceae and Pseudomonadaceae, bacterial families from PETL previously reported to be highly multidrug resistant, were the dominant families in aeration tank samples. Despite regular addition of human sewage (approximately 20%) to uphold microbial activity, the bacterial diversity within aeration tanks from PETL was considerably lower than corresponding samples from seven, regular municipal waste water treatment plants. The strong selection pressure from antibiotics present may be one important factor in structuring the microbial community in PETL, which may affect not only resistance promotion but also general efficiency of the waste treatment process.

Limited Bacterial Diversity within a Treatment Plant Receiving Antibiotic-Containing Waste from Bulk Drug Production

PubMed Central

Shouche, Yogesh S.; Larsson, D. G. Joakim

2016-01-01

Biological treatment of waste water from bulk drug production, contaminated with high levels of fluoroquinolone antibiotics, can lead to massive enrichment of antibiotic resistant bacteria, resistance genes and associated mobile elements, as previously shown. Such strong selection may be boosted by the use of activated sludge (AS) technology, where microbes that are able to thrive on the chemicals within the wastewater are reintroduced at an earlier stage of the process to further enhance degradation of incoming chemicals. The microbial community structure within such a treatment plant is, however, largely unclear. In this study, Illumina-based 16S rRNA amplicon sequencing was applied to investigate the bacterial communities of different stages from an Indian treatment plant operated by Patancheru Environment Technology Limited (PETL) in Hyderabad, India. The plant receives waste water with high levels of fluoroquinolones and applies AS technology. A total of 1,019,400 sequences from samples of different stages of the treatment process were analyzed. In total 202, 303, 732, 652, 947 and 864 operational taxonomic units (OTUs) were obtained at 3% distance cutoff in the equilibrator, aeration tanks 1 and 2, settling tank, secondary sludge and old sludge samples from PETL, respectively. Proteobacteria was the most dominant phyla in all samples with Gammaproteobacteria and Betaproteobacteria being the dominant classes. Alcaligenaceae and Pseudomonadaceae, bacterial families from PETL previously reported to be highly multidrug resistant, were the dominant families in aeration tank samples. Despite regular addition of human sewage (approximately 20%) to uphold microbial activity, the bacterial diversity within aeration tanks from PETL was considerably lower than corresponding samples from seven, regular municipal waste water treatment plants. The strong selection pressure from antibiotics present may be one important factor in structuring the microbial community in PETL, which may affect not only resistance promotion but also general efficiency of the waste treatment process. PMID:27812209

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.

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

Effect of structured teaching programme on VIA test for early detection and diagnosis of cervical cancer.

PubMed

Chacko, Shiny

2014-01-01

The conceptual framework of the study, undertaken in select health centres of New Delhi, was based on General System Model. The research approach was evaluative with one group pre-test and post-test design. The study population comprised of Community Health Workers working in selected centres in Najafgarh, Delhi. Purposive sampling technique was used to select a sample of 30 Community Health Workers. A structured knowledge questionnaire was developed to assess the knowledge of subjects. A Structured Teaching Programme was developed to enhance the knowledge of Community Health Workers. Pre-test was given on day 1 and Structured Teaching Programme administered on same day. Post-test was conducted on day 7. Most of the Community Health Workers were in the age group of 21-30 years with academic qualification up to Higher Secondary level. Maximum Community Health Workers had professional qualification as ANM/MPHW (female). Majority of the Community Health Workers had experience up to 5 years. Initially there was deficit in scores of knowledge of Community Health Workers regarding Visual Inspection with Acetic Acid (VIA) test. Mean post-test knowledge scores of Community Health Workers were found to be signifi- cantly higher than their mean pre-test knowledge score. The Community Health Workers after expo- sure to Structured Teaching Programme gained a significant positive relationship between post-test knowledge scores. The study reveals the efficacy of Structured Teaching Programme in enhancing the knowledge of Community Health Workers regarding VIA test and a need for conducting a regular and well planned health teaching programme on VIA test for improving their knowledge on VIA test for the early detection and diagnosis of cervical cancer.

Recombinant production and solution structure of lipid transfer protein from lentil Lens culinaris

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

Gizatullina, Albina K.; Moscow Institute of Physics and Technology; Finkina, Ekaterina I.

2013-10-04

Highlights: •Lipid transfer protein from lentil seeds (Lc-LTP2) was overexpressed in E. coli. •Antimicrobial activity and spatial structure of the recombinant Lc-LTP2 were examined. •Internal tunnel-like lipid-binding cavity occupies ∼7% of the total Lc-LTP2 volume. •Binding of DMPG lipid induces moderate rearrangements in the Lc-LTP2 structure. •Lc-LTP2/DMPG complex has limited lifetime and dissociates within tens of hours. -- Abstract: Lipid transfer protein, designated as Lc-LTP2, was isolated from seeds of the lentil Lens culinaris. The protein has molecular mass 9282.7 Da, consists of 93 amino acid residues including 8 cysteines forming 4 disulfide bonds. Lc-LTP2 and its stable isotope labeledmore » analogues were overexpressed in Escherichia coli and purified. Antimicrobial activity of the recombinant protein was examined, and its spatial structure was studied by NMR spectroscopy. The polypeptide chain of Lc-LTP2 forms four α-helices (Cys4-Leu18, Pro26-Ala37, Thr42-Ala56, Thr64-Lys73) and a long C-terminal tail without regular secondary structure. Side chains of the hydrophobic residues form a relatively large internal tunnel-like lipid-binding cavity (van der Waals volume comes up to ∼600 Å{sup 3}). The side-chains of Arg45, Pro79, and Tyr80 are located near an assumed mouth of the cavity. Titration with dimyristoyl phosphatidylglycerol (DMPG) revealed formation of the Lc-LTP2/lipid non-covalent complex accompanied by rearrangements in the protein spatial structure and expansion of the internal cavity. The resultant Lc-LTP2/DMPG complex demonstrates limited lifetime and dissociates within tens of hours.« less

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.

[The Role of Calcium in the Conformational Changes of the Recombinant S100A8/S100A9].

PubMed

Gheibi, N; Asghari, H; Chegini, K G; Sahmani, M; Moghadasi, M

2016-01-01

Calprotectin is a member of the EF-hand proteins, composed of two subunits, S100A8 (MRP8) and S100A9 (MRP14). These proteins are involved in important processes including cell signaling, regulation of inflammatory responses, cell cycle control, differentiation, regulation of ion channel activity and defense against microbial agents in a calcium dependent manner. In the present study, recombinant S100A8 and S100A9 were expressed in E. coli BL21 and then purified using Ni-NTA affinity chromatography. The structure of the S100A8/A9 complex in the presence and absence of calcium was assessed by circular dichroism and fluorescence spectroscopy. The intrinsic fluorescence emission spectra of the S100A8/A9 complex in the presence of calcium showed a reduction in fluorescence intensity, reflecting conformational changes within the protein with the exposure of aromatic residues to the protein surface. The far ultraviolet-circular dichroism spectra of the complex in the presence of calcium revealed minor changes in the regular secondary structure of the complex. Also, increased thermal stability of the S100A8/A9 complex in the presence of calcium was indicated.

The role of protein homochirality in shaping the energy landscape of folding

PubMed Central

Nanda, Vikas; Andrianarijaona, Aina; Narayanan, Chitra

2007-01-01

The homochirality, or isotacticity, of the natural amino acids facilitates the formation of regular secondary structures such as α-helices and β-sheets. However, many examples exist in nature where novel polypeptide topologies use both l- and d-amino acids. In this study, we explore how stereochemistry of the polypeptide backbone influences basic properties such as compactness and the size of fold space by simulating both lattice and all-atom polypeptide chains. We formulate a rectangular lattice chain model in both two and three dimensions, where monomers are chiral, having the effect of restricting local conformation. Syndiotactic chains with alternating chirality of adjacent monomers have a very large ensemble of accessible conformations characterized predominantly by extended structures. Isotactic chains on the other hand, have far fewer possible conformations and a significant fraction of these are compact. Syndiotactic chains are often unable to access maximally compact states available to their isotactic counterparts of the same length. Similar features are observed in all-atom models of isotactic versus syndiotactic polyalanine. Our results suggest that protein isotacticity has evolved to increase the enthalpy of chain collapse by facilitating compact helical states and to reduce the entropic cost of folding by restricting the size of the unfolded ensemble of competing states. PMID:17600146

A multivariate prediction model for Rho-dependent termination of transcription.

PubMed

Nadiras, Cédric; Eveno, Eric; Schwartz, Annie; Figueroa-Bossi, Nara; Boudvillain, Marc

2018-06-21

Bacterial transcription termination proceeds via two main mechanisms triggered either by simple, well-conserved (intrinsic) nucleic acid motifs or by the motor protein Rho. Although bacterial genomes can harbor hundreds of termination signals of either type, only intrinsic terminators are reliably predicted. Computational tools to detect the more complex and diversiform Rho-dependent terminators are lacking. To tackle this issue, we devised a prediction method based on Orthogonal Projections to Latent Structures Discriminant Analysis [OPLS-DA] of a large set of in vitro termination data. Using previously uncharacterized genomic sequences for biochemical evaluation and OPLS-DA, we identified new Rho-dependent signals and quantitative sequence descriptors with significant predictive value. Most relevant descriptors specify features of transcript C>G skewness, secondary structure, and richness in regularly-spaced 5'CC/UC dinucleotides that are consistent with known principles for Rho-RNA interaction. Descriptors collectively warrant OPLS-DA predictions of Rho-dependent termination with a ∼85% success rate. Scanning of the Escherichia coli genome with the OPLS-DA model identifies significantly more termination-competent regions than anticipated from transcriptomics and predicts that regions intrinsically refractory to Rho are primarily located in open reading frames. Altogether, this work delineates features important for Rho activity and describes the first method able to predict Rho-dependent terminators in bacterial genomes.

Improvements to robotics-inspired conformational sampling in rosetta.

PubMed

Stein, Amelie; Kortemme, Tanja

2013-01-01

To accurately predict protein conformations in atomic detail, a computational method must be capable of sampling models sufficiently close to the native structure. All-atom sampling is difficult because of the vast number of possible conformations and extremely rugged energy landscapes. Here, we test three sampling strategies to address these difficulties: conformational diversification, intensification of torsion and omega-angle sampling and parameter annealing. We evaluate these strategies in the context of the robotics-based kinematic closure (KIC) method for local conformational sampling in Rosetta on an established benchmark set of 45 12-residue protein segments without regular secondary structure. We quantify performance as the fraction of sub-Angstrom models generated. While improvements with individual strategies are only modest, the combination of intensification and annealing strategies into a new "next-generation KIC" method yields a four-fold increase over standard KIC in the median percentage of sub-Angstrom models across the dataset. Such improvements enable progress on more difficult problems, as demonstrated on longer segments, several of which could not be accurately remodeled with previous methods. Given its improved sampling capability, next-generation KIC should allow advances in other applications such as local conformational remodeling of multiple segments simultaneously, flexible backbone sequence design, and development of more accurate energy functions.

Improvements to Robotics-Inspired Conformational Sampling in Rosetta

PubMed Central

Stein, Amelie; Kortemme, Tanja

2013-01-01

To accurately predict protein conformations in atomic detail, a computational method must be capable of sampling models sufficiently close to the native structure. All-atom sampling is difficult because of the vast number of possible conformations and extremely rugged energy landscapes. Here, we test three sampling strategies to address these difficulties: conformational diversification, intensification of torsion and omega-angle sampling and parameter annealing. We evaluate these strategies in the context of the robotics-based kinematic closure (KIC) method for local conformational sampling in Rosetta on an established benchmark set of 45 12-residue protein segments without regular secondary structure. We quantify performance as the fraction of sub-Angstrom models generated. While improvements with individual strategies are only modest, the combination of intensification and annealing strategies into a new “next-generation KIC” method yields a four-fold increase over standard KIC in the median percentage of sub-Angstrom models across the dataset. Such improvements enable progress on more difficult problems, as demonstrated on longer segments, several of which could not be accurately remodeled with previous methods. Given its improved sampling capability, next-generation KIC should allow advances in other applications such as local conformational remodeling of multiple segments simultaneously, flexible backbone sequence design, and development of more accurate energy functions. PMID:23704889

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

CONTROL FUNCTION ASSISTED IPW ESTIMATION WITH A SECONDARY OUTCOME IN CASE-CONTROL STUDIES.

PubMed

Sofer, Tamar; Cornelis, Marilyn C; Kraft, Peter; Tchetgen Tchetgen, Eric J

2017-04-01

Case-control studies are designed towards studying associations between risk factors and a single, primary outcome. Information about additional, secondary outcomes is also collected, but association studies targeting such secondary outcomes should account for the case-control sampling scheme, or otherwise results may be biased. Often, one uses inverse probability weighted (IPW) estimators to estimate population effects in such studies. IPW estimators are robust, as they only require correct specification of the mean regression model of the secondary outcome on covariates, and knowledge of the disease prevalence. However, IPW estimators are inefficient relative to estimators that make additional assumptions about the data generating mechanism. We propose a class of estimators for the effect of risk factors on a secondary outcome in case-control studies that combine IPW with an additional modeling assumption: specification of the disease outcome probability model. We incorporate this model via a mean zero control function. We derive the class of all regular and asymptotically linear estimators corresponding to our modeling assumption, when the secondary outcome mean is modeled using either the identity or the log link. We find the efficient estimator in our class of estimators and show that it reduces to standard IPW when the model for the primary disease outcome is unrestricted, and is more efficient than standard IPW when the model is either parametric or semiparametric.

Providing Students with Foundational Field Instruction within a 50 Minute Class Period: A Practical Example

NASA Astrophysics Data System (ADS)

Percy, M.

2014-12-01

There is a growing recognition among secondary educators and administrators that students need to have a science education that provides connections between familiar classes like biology, chemistry, and physics. Because of this waxing interest in an integrative approach to the sciences, there is a broader push for school districts to offer classes geared towards the earth sciences, a field that incorporates knowledge and skills gleaned from the three core science subjects. Within the contexts of a regular secondary school day on a traditional schedule (45- to 50-minute long classes), it is challenging to engage students in rigorous field-based learning, critical for students to develop a deeper understanding of geosciences content, without requiring extra time outside of the regular schedule. We suggest instruction using common, manmade features like drainage retention ponds to model good field practices and provide students with the opportunity to calculate basic hydrologic budgets, take pH readings, and, if in an area with seasonal rainfall, make observations regarding soils by way of trenching, and near-surface processes, including mass wasting and the effects of vegetation on geomorphology. Gains in student understanding are discussed by analyzing the difference in test scores between exams provided to the students after they had received only in-class instruction, and after they had received field instruction in addition to the in-class lectures. In an advanced setting, students made measurements regarding ion contents and pollution that allowed the classes to practice lab skills while developing a data set that was analyzed after field work was completed. It is posited that similar fieldwork could be an effective approach at an introductory level in post-secondary institutions.

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/ .

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).

Secondary School Mathematics Special Edition, Chapter 12. Similarity, Chapter 13. More About Rational Numbers, Chapter 14. Perpendiculars, Student's Text.

ERIC Educational Resources Information Center

DeVenney, William S.; And Others

This text is one of the sequence of textbooks produced for low achievers in the seventh and eighth grades by the School Mathematics Study Group (SMSG). There are eight texts in the sequence, of which this is the sixth. This set of volumes differs from the regular editions of SMSG junior high school texts in that very little reading is required.…

Educational Programs That Work. Volume 1: A Catalogue of Demonstration Sites of Successful Educational Programs Disseminated through the New Jersey Elementary and Secondary Education Act, Title III, IV-C Program. 1975-76 Edition.

ERIC Educational Resources Information Center

Soper, Dorothy B.

Contained in the catalogue are descriptions of 16 New Jersey public school regular and special education programs which have been shown to be successful, cost effective, and exportable. Considered are such aspects as essential program elements, goals, evaluation design, costs, dissemination services, and contact information. Among programs…

Salient Object Detection via Structured Matrix Decomposition.

PubMed

Peng, Houwen; Li, Bing; Ling, Haibin; Hu, Weiming; Xiong, Weihua; Maybank, Stephen J

2016-05-04

Low-rank recovery models have shown potential for salient object detection, where a matrix is decomposed into a low-rank matrix representing image background and a sparse matrix identifying salient objects. Two deficiencies, however, still exist. First, previous work typically assumes the elements in the sparse matrix are mutually independent, ignoring the spatial and pattern relations of image regions. Second, when the low-rank and sparse matrices are relatively coherent, e.g., when there are similarities between the salient objects and background or when the background is complicated, it is difficult for previous models to disentangle them. To address these problems, we propose a novel structured matrix decomposition model with two structural regularizations: (1) a tree-structured sparsity-inducing regularization that captures the image structure and enforces patches from the same object to have similar saliency values, and (2) a Laplacian regularization that enlarges the gaps between salient objects and the background in feature space. Furthermore, high-level priors are integrated to guide the matrix decomposition and boost the detection. We evaluate our model for salient object detection on five challenging datasets including single object, multiple objects and complex scene images, and show competitive results as compared with 24 state-of-the-art methods in terms of seven performance metrics.

Pokémon Go: digital health interventions to reduce cardiovascular risk.

PubMed

Krittanawong, Chayakrit; Aydar, Mehmet; Kitai, Takeshi

2017-10-01

Physical activity is associated with a lower risk of coronary heart disease/cardiovascular disease mortality, and current guidelines recommend physical activity for primary prevention in healthy individuals and secondary prevention in patients with coronary heart disease/cardiovascular disease. Over the last decade, playing classic video games has become one of the most popular leisure activities in the world, but is associated with a sedentary lifestyle. In the new era of rapidly evolving augmented reality technology, Pokémon Go, a well-known augmented reality game, may promote physical activity and prevent cardiovascular disease risks - that is, diabetes, obesity, and hypertension. Pokémon Go makes players willing to be physically active for regular and long periods of time. We report on an assessment of regular walking and playing Pokémon Go by performing data mining in Twitter.

Rhythm's Gonna Get You: Regular Meter Facilitates Semantic Sentence Processing

ERIC Educational Resources Information Center

Rothermich, Kathrin; Schmidt-Kassow, Maren; Kotz, Sonja A.

2012-01-01

Rhythm is a phenomenon that fundamentally affects the perception of events unfolding in time. In language, we define "rhythm" as the temporal structure that underlies the perception and production of utterances, whereas "meter" is defined as the regular occurrence of beats (i.e. stressed syllables). In stress-timed languages such as German, this…

Schnek: A C++ library for the development of parallel simulation codes on regular grids

NASA Astrophysics Data System (ADS)

Schmitz, Holger

2018-05-01

A large number of algorithms across the field of computational physics are formulated on grids with a regular topology. We present Schnek, a library that enables fast development of parallel simulations on regular grids. Schnek contains a number of easy-to-use modules that greatly reduce the amount of administrative code for large-scale simulation codes. The library provides an interface for reading simulation setup files with a hierarchical structure. The structure of the setup file is translated into a hierarchy of simulation modules that the developer can specify. The reader parses and evaluates mathematical expressions and initialises variables or grid data. This enables developers to write modular and flexible simulation codes with minimal effort. Regular grids of arbitrary dimension are defined as well as mechanisms for defining physical domain sizes, grid staggering, and ghost cells on these grids. Ghost cells can be exchanged between neighbouring processes using MPI with a simple interface. The grid data can easily be written into HDF5 files using serial or parallel I/O.

Finite element based contact analysis of radio frequency MEMs switch membrane surfaces

NASA Astrophysics Data System (ADS)

Liu, Jin-Ya; Chalivendra, Vijaya; Huang, Wenzhen

2017-10-01

Finite element simulations were performed to determine the contact behavior of radio frequency (RF) micro-electro-mechanical (MEM) switch contact surfaces under monotonic and cyclic loading conditions. Atomic force microscopy (AFM) was used to capture the topography of RF-MEM switch membranes and later they were analyzed for multi-scale regular as well as fractal structures. Frictionless, non-adhesive contact 3D finite element analysis was carried out at different length scales to investigate the contact behavior of the regular-fractal surface using an elasto-plastic material model. Dominant micro-scale regular patterns were found to significantly change the contact behavior. Contact areas mainly cluster around the regular pattern. The contribution from the fractal structure is not significant. Under cyclic loading conditions, plastic deformation in the 1st loading/unloading cycle smooth the surface. The subsequent repetitive loading/unloading cycles undergo elastic contact without changing the morphology of the contacting surfaces. The work is expected to shed light on the quality of the switch surface contact as well as the optimum design of RF MEM switch surfaces.

Cooperation in the noisy case: Prisoner's dilemma game on two types of regular random graphs

NASA Astrophysics Data System (ADS)

Vukov, Jeromos; Szabó, György; Szolnoki, Attila

2006-06-01

We have studied an evolutionary prisoner’s dilemma game with players located on two types of random regular graphs with a degree of 4. The analysis is focused on the effects of payoffs and noise (temperature) on the maintenance of cooperation. When varying the noise level and/or the highest payoff, the system exhibits a second-order phase transition from a mixed state of cooperators and defectors to an absorbing state where only defectors remain alive. For the random regular graph (and Bethe lattice) the behavior of the system is similar to those found previously on the square lattice with nearest neighbor interactions, although the measure of cooperation is enhanced by the absence of loops in the connectivity structure. For low noise the optimal connectivity structure is built up from randomly connected triangles.

Back to the basics: regular exercise matters in parkinson's disease: results from the National Parkinson Foundation QII registry study.

PubMed

Oguh, O; Eisenstein, A; Kwasny, M; Simuni, T

2014-11-01

There is a substantial interest in the impact of exercise on reduction of disability and rate of progression of Parkinson's disease (PD). The primary aim was to describe exercise habits of PD patients and factors associated with greater levels of exercise. The secondary aim was to explore whether regular exercise is associated with a slower decline of function, disease-related quality of life, and caregiver burden. The National Parkinson's Foundation (NPF) QII Registry data was used to analyze variables that correlate with levels of exercise in PD patients across disease severity. Subjects were categorized into three groups: non-exercisers (0 min/week), low exercisers (1-150 min/week), and regular exercisers (>150 min/week). Health related outcomes, disease metrics, and demographic factors associated with exercise were examined using bivariate analyses. Multiple regression models controlled for disease duration, severity, and cognitive function. An exploratory analysis was completed on the association of baseline level of exercise with health outcomes at one year follow up. 4866 subjects were included in the baseline analysis and 2252 subjects who had second visits were included in the longitudinal data. Regular exercisers at baseline were associated with better QOL, mobility, and physical function, less progression of disease, less caregiver burden and less cognitive decline one year later, after controlling for demographic and disease severity variables. This study provides important preliminary evidence of the beneficial effects of regular exercise in a large PD cohort. Longitudinal studies will be essential to confirm findings. Copyright © 2014 Elsevier Ltd. All rights reserved.

Further investigation on "A multiplicative regularization for force reconstruction"

NASA Astrophysics Data System (ADS)

Aucejo, M.; De Smet, O.

2018-05-01

We have recently proposed a multiplicative regularization to reconstruct mechanical forces acting on a structure from vibration measurements. This method does not require any selection procedure for choosing the regularization parameter, since the amount of regularization is automatically adjusted throughout an iterative resolution process. The proposed iterative algorithm has been developed with performance and efficiency in mind, but it is actually a simplified version of a full iterative procedure not described in the original paper. The present paper aims at introducing the full resolution algorithm and comparing it with its simplified version in terms of computational efficiency and solution accuracy. In particular, it is shown that both algorithms lead to very similar identified solutions.

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.

Role of organic matter on aggregate stability and related mechanisms through organic amendments

NASA Astrophysics Data System (ADS)

Zaher, Hafida

2010-05-01

To date, only a few studies have tried to simultaneously compare the role of neutral and uronic sugars and lipids on soil structural stability. Moreover, evidence for the mechanisms involved has often been established following wetting of moist aggregates after various pre-treatments thus altering aggregate structure and resulting in manipulations on altered aggregates on which the rapid wetting process may not be involved anymore. To the best of our knowledge, the objective of this work was to study the role of neutral and uronic sugars and lipids in affecting key mechanisms (swelling rate, pressure evolution) involved in the stabilization of soil structure. A long-term incubation study (48-wk) was performed on a clay loam and a silty-clay loam amended with de-inking-secondary sludge mix at three rates (8, 16 and 24 Mg dry matter ha-1), primary-secondary sludge mix at one rate (18 Mg oven-dry ha-1) and composted de-inking sludge at one rate (24 Mg ha-1). Different structural stability indices (stability of moist and dry aggregates, the amount of dispersible clay and loss of soil material following sudden wetting) were measured on a regular basis during the incubation, along with CO2 evolved, neutral and uronic sugar, and lipid contents. During the course of the incubations, significant increases in all stability indices were measured for both soil types. In general, the improvements in stability were proportional to the amount of C added as organic amendments. These improvements were linked to a very intense phase of C mineralization and associated with increases in neutral and uronic sugars as well as lipid contents. The statistical relationships found between the different carbonaceous fractions and stability indices were all highly significant and indicated no clear superiority of one fraction over another. Paper sludge amendments also resulted in significant decreases in maximum internal pressure of aggregate and aggregate swelling following immersion in water, two mechanisms affecting structural stability. Overall, the results suggest that reduction in maximum internal pressure induced by organic amendments most likely resulted from increases in pore surface roughness and pore occlusion rather than by increase in surface wetting angles. This study also supports the view of a non specific action of the lipids, neutral and uronic sugars on aggregate stability to rapid wetting. Key words: soil aggregate stability, polysaccharides, lipids, mechanisms, organic matter

Examining physiotherapist use of structured aerobic exercise testing to decrease barriers to aerobic exercise.

PubMed

Foster B Sc, Evan; Fraser, Julia E; Inness PhD, Elizabeth L; Munce, Sarah; Biasin, Louis; Poon, Vivien; Bayley, Mark

2018-04-03

To determine the frequency of physiotherapist-administered aerobic exercise testing/training, the proportion of physiotherapists who administer this testing/training, and the barriers that currently exist across different practice environments. A secondary objective is to identify the learning needs of physiotherapists for the development of an education curriculum in aerobic exercise testing and training with electrocardiograph (ECG) administration and interpretation. National, cross-sectional survey. Registered physiotherapists practicing in Canada. Out of 137 participants, most (75%) physiotherapists prescribed aerobic exercise on a regular basis (weekly); however, 65% had never conducted an aerobic exercise test. There were no significant differences in frequency of aerobic exercise testing across different practice environments or across years of physiotherapy experience. Physiotherapists perceived the main barriers to aerobic exercise testing as being a lack of equipment/space (78%), time (65%), and knowledge (56%). Although most (82%) were uncomfortable administering 12-lead ECG-monitored aerobic exercise tests, 60% stated they would be interested in learning more about ECG interpretation. This study found that physiotherapists are regularly implementing aerobic exercise. This exercise was infrequently guided by formal aerobic exercise testing, which could increase access to safe and effective exercise within the optimal aerobic training zone. As well, this could facilitate training in patients with cardiovascular diagnoses that require additional testing for medical clearance. Increased ECG training and access to equipment for physiotherapists may augment pre-screening aerobic exercise testing. This training should include learning the key arrhythmias for aerobic exercise test termination as defined by the American College of Sports Medicine.

Crystallization mechanisms of acicular crystals

NASA Astrophysics Data System (ADS)

Puel, François; Verdurand, Elodie; Taulelle, Pascal; Bebon, Christine; Colson, Didier; Klein, Jean-Paul; Veesler, Stéphane

2008-01-01

In this contribution, we present an experimental investigation of the growth of four different organic molecules produced at industrial scale with a view to understand the crystallization mechanism of acicular or needle-like crystals. For all organic crystals studied in this article, layer-by-layer growth of the lateral faces is very slow and clear, as soon as the supersaturation is high enough, there is competition between growth and surface-activated secondary nucleation. This gives rise to pseudo-twinned crystals composed of several needle individuals aligned along a crystallographic axis; this is explained by regular over- and inter-growths as in the case of twinning. And when supersaturation is even higher, nucleation is fast and random. In an industrial continuous crystallization, the rapid growth of needle-like crystals is to be avoided as it leads to fragile crystals or needles, which can be partly broken or totally detached from the parent crystals especially along structural anisotropic axis corresponding to weaker chemical bonds, thus leading to slower growing faces. When an activated mechanism is involved such as a secondary surface nucleation, it is no longer possible to obtain a steady state. Therefore, the crystal number, size and habit vary significantly with time, leading to troubles in the downstream processing operations and to modifications of the final solid-specific properties. These results provide valuable information on the unique crystallization mechanisms of acicular crystals, and show that it is important to know these threshold and critical values when running a crystallizer in order to obtain easy-to-handle crystals.

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

Alite-ye'elimite cement: Synthesis and mineralogical analysis

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

Ma, Suhua; Snellings, Ruben; Li, Xuerun

2013-03-15

Alite-ye'elimite cement is an alternative cement that combines desirable characteristics of calcium sulfoaluminate cements and Portland cement in that it shows improved strength development at early age while retaining high portlandite contents. The key problem in the clinkering process is to produce the alite-ye'elimite phase assemblage so that both phases can co-exist. In this study, a new synthesis method is proposed to achieve the coexistence of alite and ye'elimite consisting of a secondary heat treatment step at 1250 °C after regular Portland clinker firing at 1450 °C. Quantitative X-ray powder diffraction and electron microscopy were used to analyze the phasemore » composition of clinker before and after the secondary heat treatment. The results show that ye'elimite develops during secondary heat treatment of calcium sulphate enriched clinker by reaction of C{sub 3}A and sulphate phases. Additional ferrite is formed as result of rejection of Fe originally in solid solution with C{sub 3}A during ye'elimite formation.« less

Uncultured microorganisms as a source of secondary metabolites.

PubMed

Lewis, Kim; Epstein, Slava; D'Onofrio, Anthony; Ling, Losee L

2010-08-01

The vast majority of microbial species are 'uncultured' and do not grow under laboratory conditions. This has led to the development of a number of methods to culture these organisms in a simulated natural environment. Approaches include placing cells in chambers that allow diffusion of compounds from the natural environment, traps enclosed with porous membranes that specifically capture organisms forming hyphae--actinobacteria and microfungi, and growth in the presence of cultivable helper species. Repeated cultivation in situ produces domesticated variants that can grow on regular media in vitro, and can be scaled up for secondary metabolite production. The co-culture approach has led to the identification of the first class of growth factors for uncultured bacteria, iron-chelating siderophores. It appears that many uncultured organisms from diverse taxonomical groups have lost the ability to produce siderophores, and depend on neighboring species for growth. The new cultivation approaches allow for the exploitation of the secondary metabolite potential of the previously inaccessible microorganisms.

Severe propylene glycol toxicity secondary to use of anti-epileptics.

PubMed

Pillai, Unnikrishnan; Hothi, Jatinder C; Bhat, Zeenat Y

2014-01-01

Propylene glycol toxicity presenting as high anion gap metabolic acidosis and osmolar gap has been extensively reported in literature, and most of them are secondary to intravenous lorazepam infusion. However, propylene glycol is used as a solvent in a number of medications that are frequently utilized in critical care setting, and hence one should be aware that the toxicity is possible from a variety of medication. Phenobarbital and phenytoin are one of those, and we hereby report a novel case of propylene glycol toxicity secondary to phenobarbital and phenytoin infusion in a patient with refractory status epilepticus. Furthermore, our patient had end-stage renal disease, which we think could have been an important precipitating factor for the toxicity. Because most of the symptoms from propylene glycol toxicity can mimic sepsis-which is very common in critical care unit patients-this life threatening scenario could be easily missed. Regular monitoring of osmolar gap is an easily available intervention in the at risk patients.

Long-term study of smoking by secondary schoolchildren.

PubMed Central

Banks, M H; Bewley, B R; Bland, J M; Dean, J R; Pollard, V

1978-01-01

We report the methodology and some first year results of a 5-year longitudinal study of smoking. In 6330 Derbyshire secondary schoolchildren aged 11-16 years, 6% of boys and 2.5% of girls were smoking one or more cigarettes per week. Higher rates of regular smoking and of children who had tried smoking were found in secondary modern schools, followed by middle, comprehensive and grammar schools. The results clarify the relationship between children's smoking habits and those of the parents and siblings. Boys were more likely to smoke if their fathers smoked and girls were more likely to smoke if their mothers smoked. Irrespective of parental smoking, whether or not siblings smoked had a great influence on whether the child would smoke. Having more money to spend, working at a part-time job, spending more evenings out with a mixed-sex peer group, at a youth club, or out dancing, and playing truant from school were all associated with an increased risk of smoking. PMID:626513

Mechanisms of high-regularity periodic structuring of silicon surface by sub-MHz repetition rate ultrashort laser pulses

NASA Astrophysics Data System (ADS)

Gnilitskyi, Iaroslav; Gruzdev, Vitaly; Bulgakova, Nadezhda M.; Mocek, Tomáš; Orazi, Leonardo

2016-10-01

Silicon is one of the most abundant materials which is used in many areas of modern research and technology. A variety of those applications require surface nanopatterning with minimum structure defects. However, the high-quality nanostructuring of large areas of silicon surface at industrially acceptable speed is still a challenge. Here, we report a rapid formation of highly regular laser-induced periodic surface structures (HR-LIPSS) in the regime of strong ablation by infrared femtosecond laser pulses at sub-MHz repetition rate. Parameters of the laser-surface interactions and obtained experimental results suggest an important role of electrostatically assisted bond softening in initiating the HR-LIPSS formation.

Spacecraft hazard avoidance utilizing structured light

NASA Technical Reports Server (NTRS)

Liebe, Carl Christian; Padgett, Curtis; Chapsky, Jacob; Wilson, Daniel; Brown, Kenneth; Jerebets, Sergei; Goldberg, Hannah; Schroeder, Jeffrey

2006-01-01

At JPL, a <5 kg free-flying micro-inspector spacecraft is being designed for host-vehicle inspection. The spacecraft includes a hazard avoidance sensor to navigate relative to the vehicle being inspected. Structured light was selected for hazard avoidance because of its low mass and cost. Structured light is a method of remote sensing 3-dimensional structure of the proximity utilizing a laser, a grating, and a single regular APS camera. The laser beam is split into 400 different beams by a grating to form a regular spaced grid of laser beams that are projected into the field of view of an APS camera. The laser source and the APS camera are separated forming the base of a triangle. The distance to all beam intersections of the host are calculated based on triangulation.

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…