Enhancing the Alignment of the Preclinical and Clinical Stroke Recovery Research Pipeline: Consensus-Based Core Recommendations From the Stroke Recovery and Rehabilitation Roundtable Translational Working Group.

PubMed

Corbett, Dale; Carmichael, S Thomas; Murphy, Timothy H; Jones, Theresa A; Schwab, Martin E; Jolkkonen, Jukka; Clarkson, Andrew N; Dancause, Numa; Weiloch, Tadeusz; Johansen-Berg, Heidi; Nilsson, Michael; McCullough, Louise D; Joy, Mary T

2017-08-01

Stroke recovery research involves distinct biological and clinical targets compared to the study of acute stroke. Guidelines are proposed for the pre-clinical modeling of stroke recovery and for the alignment of pre-clinical studies to clinical trials in stroke recovery.

Cofactor specificity switch in Shikimate dehydrogenase by rational design and consensus engineering.

PubMed

García-Guevara, Fernando; Bravo, Iris; Martínez-Anaya, Claudia; Segovia, Lorenzo

2017-08-01

Consensus engineering has been used to design more stable variants using the most frequent amino acid at each site of a multiple sequence alignment; sometimes consensus engineering modifies function, but efforts have mainly been focused on studying stability. Here we constructed a consensus Rossmann domain for the Shikimate dehydrogenase enzyme; separately we decided to switch the cofactor specificity through rational design in the Escherichia coli Shikimate dehydrogenase enzyme and then analyzed the effect of consensus mutations on top of our design. We found that consensus mutations closest to the 2' adenine moiety increased the activity in our design. Consensus engineering has been shown to result in more stable proteins and our findings suggest it could also be used as a complementary tool for increasing or modifying enzyme activity during design. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

R2R--software to speed the depiction of aesthetic consensus RNA secondary structures.

PubMed

Weinberg, Zasha; Breaker, Ronald R

2011-01-04

With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or interactive programs specific to RNA. Unfortunately, the use of applications like Illustrator is extremely time consuming, while existing RNA-specific programs produce figures that are useful, but usually not of the same aesthetic quality as those produced at great cost in Illustrator. Additionally, most existing RNA-specific applications are designed for drawing single RNA molecules, not consensus diagrams. We created R2R, a computer program that facilitates the generation of aesthetic and readable drawings of RNA consensus diagrams in a fraction of the time required with general-purpose drawing programs. Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment, the R2R user annotates the alignment with commands directing the layout and annotation of the RNA. R2R creates SVG or PDF output that can be imported into Adobe Illustrator, Inkscape or CorelDRAW. R2R can be used to create consensus sequence and secondary structure models for novel RNA structures or to revise models when new representatives for known RNA classes become available. Although R2R does not currently have a graphical user interface, it has proven useful in our efforts to create 100 schematic models of distinct noncoding RNA classes. R2R makes it possible to obtain high-quality drawings of the consensus sequence and structural models of many diverse RNA structures with a more practical amount of effort. R2R software is available at http://breaker.research.yale.edu/R2R and as an Additional file.

System Alignment and Consensus Discourses in Reforms: "School Effectiveness Frameworks and Instructional Rounds." Philosophical Responses with Oakeshott, Mouffe and Rancière

ERIC Educational Resources Information Center

Stickney, Jeff

2015-01-01

In this commentary 26-year Ontario district teacher, Jeff Stickney, begins by surveying balanced approaches to large- and small-scale education reforms: contrasting linear alignment with more complex ecological models, drawing on recent work by Andy Hargreaves (2008; Hargreaves & Shirley, 2012). Next, through a brief case study of School…

The role of knee alignment in disease progression and functional decline in knee osteoarthritis.

PubMed

Sharma, L; Song, J; Felson, D T; Cahue, S; Shamiyeh, E; Dunlop, D D

2001-07-11

Knee osteoarthritis (OA) is a leading cause of disability in older persons. Few risk factors for disease progression or functional decline have been identified. Hip-knee-ankle alignment influences load distribution at the knee; varus and valgus alignment increase medial and lateral load, respectively. To test the hypotheses that (1) varus alignment increases risk of medial knee OA progression during the subsequent 18 months, (2) valgus alignment increases risk of subsequent lateral knee OA progression, (3) greater severity of malalignment is associated with greater subsequent loss of joint space, and (4) greater burden of malalignment is associated with greater subsequent decline in physical function. Prospective longitudinal cohort study conducted March 1997 to March 2000 at an academic medical center in Chicago, Ill. A total of 237 persons recruited from the community with primary knee OA, defined by presence of definite tibiofemoral osteophytes and at least some difficulty with knee-requiring activity; 230 (97%) completed the study. Progression of OA, defined as a 1-grade increase in severity of joint space narrowing on semiflexed, fluoroscopically confirmed knee radiographs; change in narrowest joint space width; and change in physical function between baseline and 18 months, compared by knee alignment at baseline. Varus alignment at baseline was associated with a 4-fold increase in the odds of medial progression, adjusting for age, sex, and body mass index (adjusted odds ratio [OR], 4.09; 95% confidence interval [CI], 2.20-7.62). Valgus alignment at baseline was associated with a nearly 5-fold increase in the odds of lateral progression (adjusted OR, 4.89; 95% CI, 2.13-11.20). Severity of varus correlated with greater medial joint space loss during the subsequent 18 months (R = 0.52; 95% CI, 0.40-0.62 in dominant knees), and severity of valgus correlated with greater subsequent lateral joint space loss (R = 0.35; 95% CI, 0.21-0.47 in dominant knees). Having alignment of more than 5 degrees (in either direction) in both knees at baseline was associated with significantly greater functional deterioration during the 18 months than having alignment of 5 degrees or less in both knees, after adjusting for age, sex, body mass index, and pain. This is, to our knowledge, the first demonstration that in primary knee OA varus alignment increases risk of medial OA progression, that valgus alignment increases risk of lateral OA progression, that burden of malalignment predicts decline in physical function, and that these effects can be detected after as little as 18 months of observation.

Preservation affinity in consensus modules among stages of HIV-1 progression.

PubMed

Mosaddek Hossain, Sk Md; Ray, Sumanta; Mukhopadhyay, Anirban

2017-03-20

Analysis of gene expression data provides valuable insights into disease mechanism. Investigating relationship among co-expression modules of different stages is a meaningful tool to understand the way in which a disease progresses. Identifying topological preservation of modular structure also contributes to that understanding. HIV-1 disease provides a well-documented progression pattern through three stages of infection: acute, chronic and non-progressor. In this article, we have developed a novel framework to describe the relationship among the consensus (or shared) co-expression modules for each pair of HIV-1 infection stages. The consensus modules are identified to assess the preservation of network properties. We have investigated the preservation patterns of co-expression networks during HIV-1 disease progression through an eigengene-based approach. We discovered that the expression patterns of consensus modules have a strong preservation during the transitions of three infection stages. In particular, it is noticed that between acute and non-progressor stages the preservation is slightly more than the other pair of stages. Moreover, we have constructed eigengene networks for the identified consensus modules and observed the preservation structure among them. Some consensus modules are marked as preserved in two pairs of stages and are analyzed further to form a higher order meta-network consisting of a group of preserved modules. Additionally, we observed that module membership (MM) values of genes within a module are consistent with the preservation characteristics. The MM values of genes within a pair of preserved modules show strong correlation patterns across two infection stages. We have performed an extensive analysis to discover preservation pattern of co-expression network constructed from microarray gene expression data of three different HIV-1 progression stages. The preservation pattern is investigated through identification of consensus modules in each pair of infection stages. It is observed that the preservation of the expression pattern of consensus modules remains more prominent during the transition of infection from acute stage to non-progressor stage. Additionally, we observed that the module membership values of genes are coherent with preserved modules across the HIV-1 progression stages.

GeneSilico protein structure prediction meta-server.

PubMed

Kurowski, Michal A; Bujnicki, Janusz M

2003-07-01

Rigorous assessments of protein structure prediction have demonstrated that fold recognition methods can identify remote similarities between proteins when standard sequence search methods fail. It has been shown that the accuracy of predictions is improved when refined multiple sequence alignments are used instead of single sequences and if different methods are combined to generate a consensus model. There are several meta-servers available that integrate protein structure predictions performed by various methods, but they do not allow for submission of user-defined multiple sequence alignments and they seldom offer confidentiality of the results. We developed a novel WWW gateway for protein structure prediction, which combines the useful features of other meta-servers available, but with much greater flexibility of the input. The user may submit an amino acid sequence or a multiple sequence alignment to a set of methods for primary, secondary and tertiary structure prediction. Fold-recognition results (target-template alignments) are converted into full-atom 3D models and the quality of these models is uniformly assessed. A consensus between different FR methods is also inferred. The results are conveniently presented on-line on a single web page over a secure, password-protected connection. The GeneSilico protein structure prediction meta-server is freely available for academic users at http://genesilico.pl/meta.

GeneSilico protein structure prediction meta-server

PubMed Central

Kurowski, Michal A.; Bujnicki, Janusz M.

2003-01-01

Rigorous assessments of protein structure prediction have demonstrated that fold recognition methods can identify remote similarities between proteins when standard sequence search methods fail. It has been shown that the accuracy of predictions is improved when refined multiple sequence alignments are used instead of single sequences and if different methods are combined to generate a consensus model. There are several meta-servers available that integrate protein structure predictions performed by various methods, but they do not allow for submission of user-defined multiple sequence alignments and they seldom offer confidentiality of the results. We developed a novel WWW gateway for protein structure prediction, which combines the useful features of other meta-servers available, but with much greater flexibility of the input. The user may submit an amino acid sequence or a multiple sequence alignment to a set of methods for primary, secondary and tertiary structure prediction. Fold-recognition results (target-template alignments) are converted into full-atom 3D models and the quality of these models is uniformly assessed. A consensus between different FR methods is also inferred. The results are conveniently presented on-line on a single web page over a secure, password-protected connection. The GeneSilico protein structure prediction meta-server is freely available for academic users at http://genesilico.pl/meta. PMID:12824313

ProfileGrids: a sequence alignment visualization paradigm that avoids the limitations of Sequence Logos.

PubMed

Roca, Alberto I

2014-01-01

The 2013 BioVis Contest provided an opportunity to evaluate different paradigms for visualizing protein multiple sequence alignments. Such data sets are becoming extremely large and thus taxing current visualization paradigms. Sequence Logos represent consensus sequences but have limitations for protein alignments. As an alternative, ProfileGrids are a new protein sequence alignment visualization paradigm that represents an alignment as a color-coded matrix of the residue frequency occurring at every homologous position in the aligned protein family. The JProfileGrid software program was used to analyze the BioVis contest data sets to generate figures for comparison with the Sequence Logo reference images. The ProfileGrid representation allows for the clear and effective analysis of protein multiple sequence alignments. This includes both a general overview of the conservation and diversity sequence patterns as well as the interactive ability to query the details of the protein residue distributions in the alignment. The JProfileGrid software is free and available from http://www.ProfileGrid.org.

R2R - software to speed the depiction of aesthetic consensus RNA secondary structures

PubMed Central

2011-01-01

Background With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or interactive programs specific to RNA. Unfortunately, the use of applications like Illustrator is extremely time consuming, while existing RNA-specific programs produce figures that are useful, but usually not of the same aesthetic quality as those produced at great cost in Illustrator. Additionally, most existing RNA-specific applications are designed for drawing single RNA molecules, not consensus diagrams. Results We created R2R, a computer program that facilitates the generation of aesthetic and readable drawings of RNA consensus diagrams in a fraction of the time required with general-purpose drawing programs. Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment, the R2R user annotates the alignment with commands directing the layout and annotation of the RNA. R2R creates SVG or PDF output that can be imported into Adobe Illustrator, Inkscape or CorelDRAW. R2R can be used to create consensus sequence and secondary structure models for novel RNA structures or to revise models when new representatives for known RNA classes become available. Although R2R does not currently have a graphical user interface, it has proven useful in our efforts to create 100 schematic models of distinct noncoding RNA classes. Conclusions R2R makes it possible to obtain high-quality drawings of the consensus sequence and structural models of many diverse RNA structures with a more practical amount of effort. R2R software is available at http://breaker.research.yale.edu/R2R and as an Additional file. PMID:21205310

A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taeda

PubMed Central

Westbrook, Jared W.; Chhatre, Vikram E.; Wu, Le-Shin; Chamala, Srikar; Neves, Leandro Gomide; Muñoz, Patricio; Martínez-García, Pedro J.; Neale, David B.; Kirst, Matias; Mockaitis, Keithanne; Nelson, C. Dana; Peter, Gary F.; Echt, Craig S.

2015-01-01

A consensus genetic map for Pinus taeda (loblolly pine) and Pinus elliottii (slash pine) was constructed by merging three previously published P. taeda maps with a map from a pseudo-backcross between P. elliottii and P. taeda. The consensus map positioned 3856 markers via genotyping of 1251 individuals from four pedigrees. It is the densest linkage map for a conifer to date. Average marker spacing was 0.6 cM and total map length was 2305 cM. Functional predictions of mapped genes were improved by aligning expressed sequence tags used for marker discovery to full-length P. taeda transcripts. Alignments to the P. taeda genome mapped 3305 scaffold sequences onto 12 linkage groups. The consensus genetic map was used to compare the genome-wide linkage disequilibrium in a population of distantly related P. taeda individuals (ADEPT2) used for association genetic studies and a multiple-family pedigree used for genomic selection (CCLONES). The prevalence and extent of LD was greater in CCLONES as compared to ADEPT2; however, extended LD with LGs or between LGs was rare in both populations. The average squared correlations, r2, between SNP alleles less than 1 cM apart were less than 0.05 in both populations and r2 did not decay substantially with genetic distance. The consensus map and analysis of linkage disequilibrium establish a foundation for comparative association mapping and genomic selection in P. taeda and P. elliottii. PMID:26068575

Alignment and the States: Three Approaches to Aligning the National Assessment of Educational Progress with State Assessments, Other Assessments, and Standards

ERIC Educational Resources Information Center

Vockley, Martha; Lang, Vockley

2009-01-01

Since 1969, the National Assessment of Educational Progress (NAEP) has been the common yardstick for measuring the progress of students' education over time across the country. Teachers, principals, parents, policymakers, and researchers all use NAEP results to assess progress and develop ways to improve education in America. To make the…

Unified Alignment of Protein-Protein Interaction Networks.

PubMed

Malod-Dognin, Noël; Ban, Kristina; Pržulj, Nataša

2017-04-19

Paralleling the increasing availability of protein-protein interaction (PPI) network data, several network alignment methods have been proposed. Network alignments have been used to uncover functionally conserved network parts and to transfer annotations. However, due to the computational intractability of the network alignment problem, aligners are heuristics providing divergent solutions and no consensus exists on a gold standard, or which scoring scheme should be used to evaluate them. We comprehensively evaluate the alignment scoring schemes and global network aligners on large scale PPI data and observe that three methods, HUBALIGN, L-GRAAL and NATALIE, regularly produce the most topologically and biologically coherent alignments. We study the collective behaviour of network aligners and observe that PPI networks are almost entirely aligned with a handful of aligners that we unify into a new tool, Ulign. Ulign enables complete alignment of two networks, which traditional global and local aligners fail to do. Also, multiple mappings of Ulign define biologically relevant soft clusterings of proteins in PPI networks, which may be used for refining the transfer of annotations across networks. Hence, PPI networks are already well investigated by current aligners, so to gain additional biological insights, a paradigm shift is needed. We propose such a shift come from aligning all available data types collectively rather than any particular data type in isolation from others.

3D-QSAR and docking studies on 4-anilinoquinazoline and 4-anilinoquinoline epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors

NASA Astrophysics Data System (ADS)

Assefa, Haregewein; Kamath, Shantaram; Buolamwini, John K.

2003-08-01

The overexpression and/or mutation of the epidermal growth factor receptor (EGFR) tyrosine kinase has been observed in many human solid tumors, and is under intense investigation as a novel anticancer molecular target. Comparative 3D-QSAR analyses using different alignments were undertaken employing comparative molecular field analysis (CoMFA) and comparative molecular similarity analysis (CoMSIA) for 122 anilinoquinazoline and 50 anilinoquinoline inhibitors of EGFR kinase. The SYBYL multifit alignment rule was applied to three different conformational templates, two obtained from a MacroModel Monte Carlo conformational search, and one from the bound conformation of erlotinib in complex with EGFR in the X-ray crystal structure. In addition, a flexible ligand docking alignment obtained with the GOLD docking program, and a novel flexible receptor-guided consensus dynamics alignment obtained with the DISCOVER program in the INSIGHTII modeling package were also investigated. 3D-QSAR models with q2 values up to 0.70 and r2 values up to 0.97 were obtained. Among the 4-anilinoquinazoline set, the q2 values were similar, but the ability of the different conformational models to predict the activities of an external test set varied considerably. In this regard, the model derived using the X-ray crystallographically determined bioactive conformation of erlotinib afforded the best predictive model. Electrostatic, hydrophobic and H-bond donor descriptors contributed the most to the QSAR models of the 4-anilinoquinazolines, whereas electrostatic, hydrophobic and H-bond acceptor descriptors contributed the most to the 4-anilinoquinoline QSAR, particularly the H-bond acceptor descriptor. A novel receptor-guided consensus dynamics alignment has also been introduced for 3D-QSAR studies. This new alignment method may incorporate to some extent ligand-receptor induced fit effects into 3D-QSAR models.

A new fast method for inferring multiple consensus trees using k-medoids.

PubMed

Tahiri, Nadia; Willems, Matthieu; Makarenkov, Vladimir

2018-04-05

Gene trees carry important information about specific evolutionary patterns which characterize the evolution of the corresponding gene families. However, a reliable species consensus tree cannot be inferred from a multiple sequence alignment of a single gene family or from the concatenation of alignments corresponding to gene families having different evolutionary histories. These evolutionary histories can be quite different due to horizontal transfer events or to ancient gene duplications which cause the emergence of paralogs within a genome. Many methods have been proposed to infer a single consensus tree from a collection of gene trees. Still, the application of these tree merging methods can lead to the loss of specific evolutionary patterns which characterize some gene families or some groups of gene families. Thus, the problem of inferring multiple consensus trees from a given set of gene trees becomes relevant. We describe a new fast method for inferring multiple consensus trees from a given set of phylogenetic trees (i.e. additive trees or X-trees) defined on the same set of species (i.e. objects or taxa). The traditional consensus approach yields a single consensus tree. We use the popular k-medoids partitioning algorithm to divide a given set of trees into several clusters of trees. We propose novel versions of the well-known Silhouette and Caliński-Harabasz cluster validity indices that are adapted for tree clustering with k-medoids. The efficiency of the new method was assessed using both synthetic and real data, such as a well-known phylogenetic dataset consisting of 47 gene trees inferred for 14 archaeal organisms. The method described here allows inference of multiple consensus trees from a given set of gene trees. It can be used to identify groups of gene trees having similar intragroup and different intergroup evolutionary histories. The main advantage of our method is that it is much faster than the existing tree clustering approaches, while providing similar or better clustering results in most cases. This makes it particularly well suited for the analysis of large genomic and phylogenetic datasets.

High-speed multiple sequence alignment on a reconfigurable platform.

PubMed

Oliver, Tim; Schmidt, Bertil; Maskell, Douglas; Nathan, Darran; Clemens, Ralf

2006-01-01

Progressive alignment is a widely used approach to compute multiple sequence alignments (MSAs). However, aligning several hundred sequences by popular progressive alignment tools requires hours on sequential computers. Due to the rapid growth of sequence databases biologists have to compute MSAs in a far shorter time. In this paper we present a new approach to MSA on reconfigurable hardware platforms to gain high performance at low cost. We have constructed a linear systolic array to perform pairwise sequence distance computations using dynamic programming. This results in an implementation with significant runtime savings on a standard FPGA.

Tools for T-RFLP data analysis using Excel.

PubMed

Fredriksson, Nils Johan; Hermansson, Malte; Wilén, Britt-Marie

2014-11-08

Terminal restriction fragment length polymorphism (T-RFLP) analysis is a DNA-fingerprinting method that can be used for comparisons of the microbial community composition in a large number of samples. There is no consensus on how T-RFLP data should be treated and analyzed before comparisons between samples are made, and several different approaches have been proposed in the literature. The analysis of T-RFLP data can be cumbersome and time-consuming, and for large datasets manual data analysis is not feasible. The currently available tools for automated T-RFLP analysis, although valuable, offer little flexibility, and few, if any, options regarding what methods to use. To enable comparisons and combinations of different data treatment methods an analysis template and an extensive collection of macros for T-RFLP data analysis using Microsoft Excel were developed. The Tools for T-RFLP data analysis template provides procedures for the analysis of large T-RFLP datasets including application of a noise baseline threshold and setting of the analysis range, normalization and alignment of replicate profiles, generation of consensus profiles, normalization and alignment of consensus profiles and final analysis of the samples including calculation of association coefficients and diversity index. The procedures are designed so that in all analysis steps, from the initial preparation of the data to the final comparison of the samples, there are various different options available. The parameters regarding analysis range, noise baseline, T-RF alignment and generation of consensus profiles are all given by the user and several different methods are available for normalization of the T-RF profiles. In each step, the user can also choose to base the calculations on either peak height data or peak area data. The Tools for T-RFLP data analysis template enables an objective and flexible analysis of large T-RFLP datasets in a widely used spreadsheet application.

Measuring the progress of capacity building in the Alberta Policy Coalition for Cancer Prevention.

PubMed

Raine, Kim D; Sosa Hernandez, Cristabel; Nykiforuk, Candace I J; Reed, Shandy; Montemurro, Genevieve; Lytvyak, Ellina; MacLellan-Wright, Mary-Frances

2014-07-01

The Alberta Policy Coalition for Cancer Prevention (APCCP) represents practitioners, policy makers, researchers, and community organizations working together to coordinate efforts and advocate for policy change to reduce chronic diseases. The aim of this research was to capture changes in the APCCP's capacity to advance its goals over the course of its operation. We adapted the Public Health Agency of Canada's validated Community Capacity-Building Tool to capture policy work. All members of the APCCP were invited to complete the tool in 2010 and 2011. Responses were analyzed using descriptive statistics and t tests. Qualitative comments were analyzed using thematic content analysis. A group process for reaching consensus provided context to the survey responses and contributed to a participatory analysis. Significant improvement was observed in eight out of nine capacity domains. Lessons learned highlight the importance of balancing volume and diversity of intersectoral representation to ensure effective participation, as well as aligning professional and economic resources. Defining involvement and roles within a coalition can be a challenging activity contingent on the interests of each sector represented. The participatory analysis enabled the group to reflect on progress made and future directions for policy advocacy. © 2013 Society for Public Health Education.

Towards a consensus definition of maternal sepsis: results of a systematic review and expert consultation.

PubMed

Bonet, Mercedes; Nogueira Pileggi, Vicky; Rijken, Marcus J; Coomarasamy, Arri; Lissauer, David; Souza, João Paulo; Gülmezoglu, Ahmet Metin

2017-05-30

There is a need for a clear and actionable definition of maternal sepsis, in order to better assess the burden of this condition, trigger timely and effective treatment and allow comparisons across facilities and countries. The objective of this study was to review maternal sepsis definitions and identification criteria and to report on the results of an expert consultation to develop a new international definition of maternal sepsis. All original and review articles and WHO documents, as well as clinical guidelines providing definitions and/or identification criteria of maternal sepsis were included. A multidisciplinary international panel of experts was surveyed through an online consultation in March-April 2016 on their opinion on the existing sepsis definitions, including new definition of sepsis proposed for the adult population (2016 Third International Consensus Definitions for Sepsis and Septic Shock) and importance of different criteria for identification of maternal sepsis. The definition was agreed using an iterative process in an expert face-to-face consensus development meeting convened by WHO and Jhpiego. Standardizing the definition of maternal sepsis and aligning it with the current understanding of sepsis in the adult population was considered a mandatory step to improve the assessment of the burden of maternal sepsis by the expert panel. The literature review and expert consultation resulted in a new WHO consensus definition "Maternal sepsis is a life-threatening condition defined as organ dysfunction resulting from infection during pregnancy, child-birth, post-abortion, or post-partum period". Plans are in progress to validate the new WHO definition of maternal sepsis in a large international population. The operationalization of the new maternal sepsis definition requires generation of a set of practical criteria to identify women with sepsis. These criteria should enable clinicians to focus on the timely initiation of actionable elements of care (administration of antimicrobials and fluids, support of vital organ functions, and referral) and improve maternal outcomes.

ProfileGrids: a sequence alignment visualization paradigm that avoids the limitations of Sequence Logos

PubMed Central

2014-01-01

Background The 2013 BioVis Contest provided an opportunity to evaluate different paradigms for visualizing protein multiple sequence alignments. Such data sets are becoming extremely large and thus taxing current visualization paradigms. Sequence Logos represent consensus sequences but have limitations for protein alignments. As an alternative, ProfileGrids are a new protein sequence alignment visualization paradigm that represents an alignment as a color-coded matrix of the residue frequency occurring at every homologous position in the aligned protein family. Results The JProfileGrid software program was used to analyze the BioVis contest data sets to generate figures for comparison with the Sequence Logo reference images. Conclusions The ProfileGrid representation allows for the clear and effective analysis of protein multiple sequence alignments. This includes both a general overview of the conservation and diversity sequence patterns as well as the interactive ability to query the details of the protein residue distributions in the alignment. The JProfileGrid software is free and available from http://www.ProfileGrid.org. PMID:25237393

Why do we treat adolescent idiopathic scoliosis? What we want to obtain and to avoid for our patients. SOSORT 2005 Consensus paper

PubMed Central

Negrini, Stefano; Grivas, Theodoros B; Kotwicki, Tomasz; Maruyama, Toru; Rigo, Manuel; Weiss, Hans Rudolf

2006-01-01

Background Medicine is a scientific art: once science is not clear, choices are made according to individual and collective beliefs that should be better understood. This is particularly true in a field like adolescent idiopathic scoliosis, where currently does not exist definitive scientific evidence on the efficacy either of conservative or of surgical treatments. Aim of the study To verify the philosophical choices on the final outcome of a group of people believing and engaged in a conservative treatment of idiopathic scoliosis. Methods We performed a multifaceted study that included a bibliometric analysis, a questionnaire, and a careful Consensus reaching procedure between experts in the conservative treatment of scoliosis (SOSORT members). Results The Consensus reaching procedure has shown to be useful: answers changed in a statistically significant way, and 9 new outcome criteria were included. The most important final outcomes were considered Aesthetics (100%), Quality of life and Disability (more than 90%), while more than 80% of preferences went to Back Pain, Psychological well-being, Progression in adulthood, Breathing function, Scoliosis Cobb degrees (radiographic lateral flexion), Needs of further treatments in adulthood. Discussion In the literature prevail outcome criteria driven by the contingent treatment needs or the possibility to have measurement systems (even if it seems that usual clinical and radiographic methods are given much more importance than more complex Disability or Quality of Life instruments). SOSORT members give importance to a wide range of outcome criteria, in which clinical and radiographic issues have the lowest importance. Conclusion We treat our patients for what they need for their future (Breathing function, Needs of further treatments in adulthood, Progression in adulthood), and their present too (Aesthetics, Disability, Quality of life). Technical matters, such as rib hump or radiographic lateral alignment and rotation, but not lateral flexion, are secondary outcomes and only instrumental to previously reported primary outcomes. We advocate a multidimensional, comprehensive evaluation of scoliosis patients, to gather all necessary data for a complete therapeutic approach, that goes beyond x-rays to reach the person and the family. PMID:16759352

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

PubMed Central

Haas, Brian J; Salzberg, Steven L; Zhu, Wei; Pertea, Mihaela; Allen, Jonathan E; Orvis, Joshua; White, Owen; Buell, C Robin; Wortman, Jennifer R

2008-01-01

EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation. PMID:18190707

Phylogenic inference using alignment-free methods for applications in microbial community surveys using 16s rRNA gene

PubMed Central

2017-01-01

The diversity of microbiota is best explored by understanding the phylogenetic structure of the microbial communities. Traditionally, sequence alignment has been used for phylogenetic inference. However, alignment-based approaches come with significant challenges and limitations when massive amounts of data are analyzed. In the recent decade, alignment-free approaches have enabled genome-scale phylogenetic inference. Here we evaluate three alignment-free methods: ACS, CVTree, and Kr for phylogenetic inference with 16s rRNA gene data. We use a taxonomic gold standard to compare the accuracy of alignment-free phylogenetic inference with that of common microbiome-wide phylogenetic inference pipelines based on PyNAST and MUSCLE alignments with FastTree and RAxML. We re-simulate fecal communities from Human Microbiome Project data to evaluate the performance of the methods on datasets with properties of real data. Our comparisons show that alignment-free methods are not inferior to alignment-based methods in giving accurate and robust phylogenic trees. Moreover, consensus ensembles of alignment-free phylogenies are superior to those built from alignment-based methods in their ability to highlight community differences in low power settings. In addition, the overall running times of alignment-based and alignment-free phylogenetic inference are comparable. Taken together our empirical results suggest that alignment-free methods provide a viable approach for microbiome-wide phylogenetic inference. PMID:29136663

Novel Bioinformatics-Based Approach for Proteomic Biomarkers Prediction of Calpain-2 & Caspase-3 Protease Fragmentation: Application to βII-Spectrin Protein

NASA Astrophysics Data System (ADS)

El-Assaad, Atlal; Dawy, Zaher; Nemer, Georges; Kobeissy, Firas

2017-01-01

The crucial biological role of proteases has been visible with the development of degradomics discipline involved in the determination of the proteases/substrates resulting in breakdown-products (BDPs) that can be utilized as putative biomarkers associated with different biological-clinical significance. In the field of cancer biology, matrix metalloproteinases (MMPs) have shown to result in MMPs-generated protein BDPs that are indicative of malignant growth in cancer, while in the field of neural injury, calpain-2 and caspase-3 proteases generate BDPs fragments that are indicative of different neural cell death mechanisms in different injury scenarios. Advanced proteomic techniques have shown a remarkable progress in identifying these BDPs experimentally. In this work, we present a bioinformatics-based prediction method that identifies protease-associated BDPs with high precision and efficiency. The method utilizes state-of-the-art sequence matching and alignment algorithms. It starts by locating consensus sequence occurrences and their variants in any set of protein substrates, generating all fragments resulting from cleavage. The complexity exists in space O(mn) as well as in O(Nmn) time, where N, m, and n are the number of protein sequences, length of the consensus sequence, and length per protein sequence, respectively. Finally, the proposed methodology is validated against βII-spectrin protein, a brain injury validated biomarker.

Defining active progressive multiple sclerosis.

PubMed

Sellebjerg, Finn; Börnsen, Lars; Ammitzbøll, Cecilie; Nielsen, Jørgen Erik; Vinther-Jensen, Tua; Hjermind, Lena Elisabeth; von Essen, Marina; Ratzer, Rikke Lenhard; Soelberg Sørensen, Per; Romme Christensen, Jeppe

2017-11-01

It is unknown whether disease activity according to consensus criteria (magnetic resonance imaging activity or clinical relapses) associate with cerebrospinal fluid (CSF) changes in progressive multiple sclerosis (MS). To compare CSF biomarkers in active and inactive progressive MS according to consensus criteria. Neurofilament light chain (NFL), myelin basic protein (MBP), IgG-index, chitinase-3-like-1 (CHI3L1), matrix metalloproteinase-9 (MMP-9), chemokine CXCL13, terminal complement complex, leukocyte counts and nitric oxide metabolites were measured in primary ( n = 26) and secondary progressive MS ( n = 26) and healthy controls ( n = 24). Progressive MS patients had higher CSF cell counts, IgG-index, CHI3L1, MMP-9, CXCL13, NFL and MBP concentrations. Active patients were younger and had higher NFL, CXCL13 and MMP-9 concentrations than inactive patients. Patients with active disease according to consensus criteria or detectable CXCL13 or MMP-9 in CSF were defined as having combined active progressive MS. These patients had increased CSF cell counts, IgG-index and MBP, NFL and CHI3L1 concentrations. Combined inactive patients only had increased IgG-index and MBP concentrations. Patients with combined active progressive MS show evidence of inflammation, demyelination and neuronal/axonal damage, whereas the remaining patients mainly show evidence of active demyelination. This challenges the idea that neurodegeneration independent of inflammation is crucial in disease progression.

Bridging the gap between content and context: establishing expert consensus on the content of an exercise training program to prevent lower-limb injuries.

PubMed

Donaldson, Alex; Cook, Jill; Gabbe, Belinda; Lloyd, David G; Young, Warren; Finch, Caroline F

2015-05-01

To achieve expert consensus on the content of an exercise training program (known as FootyFirst) to prevent lower-limb injuries. Three-round online Delphi consultation process. Community Australian Football (AF). Members of the Australian Football Leagues' Medical Officers (n = 94), physiotherapists (n = 50), and Sports Science (n = 19) Associations were invited to participate through e-mail. Five people with more general expertise in sports-related lower-limb injury prevention were also invited to participate. The primary outcome measure was the level of agreement on the appropriateness of the proposed exercises and progressions for inclusion in FootyFirst. Consensus was reached when ≥75% of experts who responded to each item agreed and strongly agreed, or disagreed and strongly disagreed, that an exercise or its progressions were appropriate to include in FootyFirst. Fifty-five experts participated in at least 1 Delphi round. In round 1, consensus was achieved that the proposed warm-up (run through and dynamic stretches) and the exercises and progressions for hamstring strength and for balance, landing, and changing direction were appropriate to include in FootyFirst. There was also consensus in round 1 that progressions for hip/core strength should be included in FootyFirst. Consensus was reached in round 2 that the revised groin strength and hip strength exercises should be included in FootyFirst. Consensus was reached for the progression of the groin strength exercises in round 3. The formal consensus development process has resulted in an evidence-informed, researcher-developed, exercise-based sports injury prevention program that is expert endorsed and specific to the context of AF. Lower-limb injuries are common in running, kicking, and contact sports like AF. These injuries are often costly to treat, and many have high rates of recurrence, making them challenging to treat clinically. Reducing these injuries is a high priority for players, teams, and medical staff. Exercise programs provide a method for primary prevention of lower-limb injuries, but they have to be evidence based, have currency with sports practitioners/clinicians, and utility for the context in which they are to be used. However, the comprehensive methods and clinical engagement processes used to develop injury prevention exercise programs have not previously been described in detail. This study describes the results of engaging clinicians and sport scientists in the development of a lower-limb sports injury prevention program for community AF, enabling the development of a program that is both evidence informed and considerate of expert clinical opinion.

The Astronomical Orientation of Ancient Greek Temples

PubMed Central

Salt, Alun M.

2009-01-01

Despite its appearing to be a simple question to answer, there has been no consensus as to whether or not the alignments of ancient Greek temples reflect astronomical intentions. Here I present the results of a survey of archaic and classical Greek temples in Sicily and compare them with temples in Greece. Using a binomial test I show strong evidence that there is a preference for solar orientations. I then speculate that differences in alignment patterns between Sicily and Greece reflect differing pressures in the expression of ethnic identity. PMID:19936239

The astronomical orientation of ancient Greek temples.

PubMed

Salt, Alun M

2009-11-19

Despite its appearing to be a simple question to answer, there has been no consensus as to whether or not the alignments of ancient Greek temples reflect astronomical intentions. Here I present the results of a survey of archaic and classical Greek temples in Sicily and compare them with temples in Greece. Using a binomial test I show strong evidence that there is a preference for solar orientations. I then speculate that differences in alignment patterns between Sicily and Greece reflect differing pressures in the expression of ethnic identity.

In Pursuit of Consensus: Disagreement and legitimization during small-group argumentation

NASA Astrophysics Data System (ADS)

Berland, Leema K.; Lee, Victor R.

2012-08-01

In recent years, an emphasis on scientific argumentation in classrooms has brought into focus collaborative consensus-building as an instructional strategy. In these situations, students with differing and competing arguments are asked to work with one another in order to establish a shared perspective. However, the literature suggests that consensus-building can be challenging for students because their interpretations of the argumentative task and context may not enable their productive engagement with counter-arguments and evidence. In this paper, our goal is to explore the ways in which interactions of students support or inhibit their consensus-building. To that end, we examine and describe three cases that represent different ways in which initially dissenting students try to work towards a consensus with their peers. Through these cases, we demonstrate that legitimization of disparate or incorrect ideas can enable students whose arguments rely on incorrect ideas to feel that their ideas were heard and valued by the rest of their group. As such, we suggest that this legitimization is important because it can help students 'save face'. This enables students to move away from the competitive and persuasive aspects of argumentation towards interactions that align more closely with sensemaking and consensus-building.

Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring

PubMed Central

2012-01-01

Background Much progress has been made in understanding the 3D structure of proteins using methods such as NMR and X-ray crystallography. The resulting 3D structures are extremely informative, but do not always reveal which sites and residues within the structure are of special importance. Recently, there are indications that multiple-residue, sub-domain structural relationships within the larger 3D consensus structure of a protein can be inferred from the analysis of the multiple sequence alignment data of a protein family. These intra-dependent clusters of associated sites are used to indicate hierarchical inter-residue relationships within the 3D structure. To reveal the patterns of associations among individual amino acids or sub-domain components within the structure, we apply a k-modes attribute (aligned site) clustering algorithm to the ubiquitin and transthyretin families in order to discover associations among groups of sites within the multiple sequence alignment. We then observe what these associations imply within the 3D structure of these two protein families. Results The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function. Conclusions Our results demonstrate that the method we present here using a k-modes site clustering algorithm based on interdependency evaluation among sites obtained from a sequence alignment of homologous proteins can provide significant insights into the complex, hierarchical inter-residue structural relationships within the 3D structure of a protein family. PMID:22793672

Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring.

PubMed

Durston, Kirk K; Chiu, David Ky; Wong, Andrew Kc; Li, Gary Cl

2012-07-13

Much progress has been made in understanding the 3D structure of proteins using methods such as NMR and X-ray crystallography. The resulting 3D structures are extremely informative, but do not always reveal which sites and residues within the structure are of special importance. Recently, there are indications that multiple-residue, sub-domain structural relationships within the larger 3D consensus structure of a protein can be inferred from the analysis of the multiple sequence alignment data of a protein family. These intra-dependent clusters of associated sites are used to indicate hierarchical inter-residue relationships within the 3D structure. To reveal the patterns of associations among individual amino acids or sub-domain components within the structure, we apply a k-modes attribute (aligned site) clustering algorithm to the ubiquitin and transthyretin families in order to discover associations among groups of sites within the multiple sequence alignment. We then observe what these associations imply within the 3D structure of these two protein families. The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function. Our results demonstrate that the method we present here using a k-modes site clustering algorithm based on interdependency evaluation among sites obtained from a sequence alignment of homologous proteins can provide significant insights into the complex, hierarchical inter-residue structural relationships within the 3D structure of a protein family.

Fuzzy adaptive iterative learning coordination control of second-order multi-agent systems with imprecise communication topology structure

NASA Astrophysics Data System (ADS)

Chen, Jiaxi; Li, Junmin

2018-02-01

In this paper, we investigate the perfect consensus problem for second-order linearly parameterised multi-agent systems (MAS) with imprecise communication topology structure. Takagi-Sugeno (T-S) fuzzy models are presented to describe the imprecise communication topology structure of leader-following MAS, and a distributed adaptive iterative learning control protocol is proposed with the dynamic of leader unknown to any of the agent. The proposed protocol guarantees that the follower agents can track the leader perfectly on [0,T] for the consensus problem. Under alignment condition, a sufficient condition of the consensus for closed-loop MAS is given based on Lyapunov stability theory. Finally, a numerical example and a multiple pendulum system are given to illustrate the effectiveness of the proposed algorithm.

Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies.

PubMed

Joseph, Agnel Praveen; Srinivasan, Narayanaswamy; de Brevern, Alexandre G

2012-09-01

Comparison of multiple protein structures has a broad range of applications in the analysis of protein structure, function and evolution. Multiple structure alignment tools (MSTAs) are necessary to obtain a simultaneous comparison of a family of related folds. In this study, we have developed a method for multiple structure comparison largely based on sequence alignment techniques. A widely used Structural Alphabet named Protein Blocks (PBs) was used to transform the information on 3D protein backbone conformation as a 1D sequence string. A progressive alignment strategy similar to CLUSTALW was adopted for multiple PB sequence alignment (mulPBA). Highly similar stretches identified by the pairwise alignments are given higher weights during the alignment. The residue equivalences from PB based alignments are used to obtain a three dimensional fit of the structures followed by an iterative refinement of the structural superposition. Systematic comparisons using benchmark datasets of MSTAs underlines that the alignment quality is better than MULTIPROT, MUSTANG and the alignments in HOMSTRAD, in more than 85% of the cases. Comparison with other rigid-body and flexible MSTAs also indicate that mulPBA alignments are superior to most of the rigid-body MSTAs and highly comparable to the flexible alignment methods. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

Progress in linear optics, non-linear optics and surface alignment of liquid crystals

NASA Astrophysics Data System (ADS)

Ong, H. L.; Meyer, R. B.; Hurd, A. J.; Karn, A. J.; Arakelian, S. M.; Shen, Y. R.; Sanda, P. N.; Dove, D. B.; Jansen, S. A.; Hoffmann, R.

We first discuss the progress in linear optics, in particular, the formulation and application of geometrical-optics approximation and its generalization. We then discuss the progress in non-linear optics, in particular, the enhancement of a first-order Freedericksz transition and intrinsic optical bistability in homeotropic and parallel oriented nematic liquid crystal cells. Finally, we discuss the liquid crystal alignment and surface effects on field-induced Freedericksz transition.

Priorities for Evaluating Palliative Care Outcomes in Intensive Care Units.

PubMed

Bakitas, Marie; Dionne-Odom, J Nicholas; Kamal, Arif; Maguire, Jennifer M

2015-09-01

Defining the quality of intensive care unit (ICU) care when patients are dying is challenging. Palliative care has been recommended to improve outcomes of dying ICU patients; however, traditional ICU quality indicators do not always align with palliative care. Evidence suggests that some aspects of ICU care improve when palliative care is integrated; however, consensus is lacking concerning the outcomes that should be measured. Overcoming challenges to measuring palliative care will require consensus development and rigorous research on the best way to evaluate ICU palliative care services. Copyright © 2015 Elsevier Inc. All rights reserved.

Insights Into Upland Cotton (Gossypium hirsutum L.) Genetic Recombination Based on 3 High-Density Single-Nucleotide Polymorphism and a Consensus Map Developed Independently With Common Parents.

PubMed

Ulloa, Mauricio; Hulse-Kemp, Amanda M; De Santiago, Luis M; Stelly, David M; Burke, John J

2017-01-01

High-density linkage maps are vital to supporting the correct placement of scaffolds and gene sequences on chromosomes and fundamental to contemporary organismal research and scientific approaches to genetic improvement, especially in paleopolyploids with exceptionally complex genomes, eg, upland cotton ( Gossypium hirsutum L., "2n = 52"). Three independently developed intraspecific upland mapping populations were analyzed to generate 3 high-density genetic linkage single-nucleotide polymorphism (SNP) maps and a consensus map using the CottonSNP63K array. The populations consisted of a previously reported F 2 , a recombinant inbred line (RIL), and reciprocal RIL population, from "Phytogen 72" and "Stoneville 474" cultivars. The cluster file provided 7417 genotyped SNP markers, resulting in 26 linkage groups corresponding to the 26 chromosomes (c) of the allotetraploid upland cotton (AD) 1 arisen from the merging of 2 genomes ("A" Old World and "D" New World). Patterns of chromosome-specific recombination were largely consistent across mapping populations. The high-density genetic consensus map included 7244 SNP markers that spanned 3538 cM and comprised 3824 SNP bins, of which 1783 and 2041 were in the A t and D t subgenomes with 1825 and 1713 cM map lengths, respectively. Subgenome average distances were nearly identical, indicating that subgenomic differences in bin number arose due to the high numbers of SNPs on the D t subgenome. Examination of expected recombination frequency or crossovers (COs) on the chromosomes within each population of the 2 subgenomes revealed that COs were also not affected by the SNPs or SNP bin number in these subgenomes. Comparative alignment analyses identified historical ancestral A t -subgenomic translocations of c02 and c03, as well as of c04 and c05. The consensus map SNP sequences aligned with high congruency to the NBI assembly of Gossypium hirsutum . However, the genomic comparisons revealed evidence of additional unconfirmed possible duplications, inversions and translocations, and unbalance SNP sequence homology or SNP sequence/loci genomic dominance, or homeolog loci bias of the upland tetraploid A t and D t subgenomes. The alignments indicated that 364 SNP-associated previously unintegrated scaffolds can be placed in pseudochromosomes of the NBI G hirsutum assembly. This is the first intraspecific SNP genetic linkage consensus map assembled in G hirsutum with a core of reproducible mendelian SNP markers assayed on different populations and it provides further knowledge of chromosome arrangement of genic and nongenic SNPs. Together, the consensus map and RIL populations provide a synergistically useful platform for localizing and identifying agronomically important loci for improvement of the cotton crop.

Expanding Public-Private Collaborations to Enhance Cancer Drug Development: A Report of the Institute of Medicine’s Workshop Series, “Implementing a National Cancer Clinical Trials System for the 21st Century”

PubMed Central

Canetta, Renzo; Nass, Sharyl J.

2014-01-01

Since their inception in the 1950s, the National Cancer Institute-funded cancer cooperative groups have been important contributors to cancer clinical and translational research. In 2010, a committee appointed by the Institute of Medicine (IOM) of the National Academy of Sciences completed a consensus review on the status of the U.S. publicly funded cancer clinical trials system. This report identified a need to reinvigorate the cooperative groups and provided recommendations for improving their effectiveness. Follow-up workshops to monitor progress were conducted by the IOM’s National Cancer Policy Forum and the American Society of Clinical Oncology (ASCO) in 2011 and 2013. One of the key recommendations of the IOM report was a call for greater collaboration among stakeholders in cancer research. In particular, more active engagement and better alignment of incentives among the cooperative groups, the National Cancer Institute, the U.S. Food and Drug Administration, and the biopharmaceutical industry were identified as essential to achieving the promise of oncology drug development. This review, based on presentations and discussion during the IOM-ASCO workshops, outlines the progress and remaining challenges of these collaborations. PMID:25326161

Expanding public-private collaborations to enhance cancer drug development: a report of the Institute of Medicine's workshop series, "Implementing a National Cancer Clinical Trials System for the 21st Century".

PubMed

Bertagnolli, Monica M; Canetta, Renzo; Nass, Sharyl J

2014-11-01

Since their inception in the 1950s, the National Cancer Institute-funded cancer cooperative groups have been important contributors to cancer clinical and translational research. In 2010, a committee appointed by the Institute of Medicine (IOM) of the National Academy of Sciences completed a consensus review on the status of the U.S. publicly funded cancer clinical trials system. This report identified a need to reinvigorate the cooperative groups and provided recommendations for improving their effectiveness. Follow-up workshops to monitor progress were conducted by the IOM's National Cancer Policy Forum and the American Society of Clinical Oncology (ASCO) in 2011 and 2013. One of the key recommendations of the IOM report was a call for greater collaboration among stakeholders in cancer research. In particular, more active engagement and better alignment of incentives among the cooperative groups, the National Cancer Institute, the U.S. Food and Drug Administration, and the biopharmaceutical industry were identified as essential to achieving the promise of oncology drug development. This review, based on presentations and discussion during the IOM-ASCO workshops, outlines the progress and remaining challenges of these collaborations. ©AlphaMed Press.

Research and development of methods and tools for achieving and maintaining consensus processes in the face of change within and among government oversight agencies. Progress report, October 1, 1992--March 31, 1994, Volume I

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

Not Available

1994-06-01

This progress report summarizes our research activities under our consensus grant. In year five, we devoted much of our activities to completing fundamental research projects delayed because of the considerably stepped-up effort in consensus processes efforts during development of DOE`s Five Year Waste Plan (FYWP). Following our work on various procedures for bringing together groups such as the State and Tribal Government Working Group and the Stakeholders` Forum (both of which provide input to the Five Year Waste Plan), we compiled a literature overview of small-group consensus gaining and a handbook for consensus decision making. We also tested the effectivenessmore » Of group decision support software, and designed a structured observation process and its related hard- and software. We completed studies on experts and the role of personality characteristics in consensus group influence. Results of these studies are included in this final report. In consensus processes research, we were unable to continue studying consensus groups in action. However, we did study ways to improve ways to improve DOE`s technological information exchange effectiveness. We also studied how a new administration identifies what its strategic mission is and how it gets support from existing EM managers. We identified selection criteria for locating the EM exhibit, and tested our audience selection model. We also further calibrated our consensus measure. Additional conference papers and papers for journal submission were completed during year five.« less

Quantitative application of the primary progressive aphasia consensus criteria.

PubMed

Wicklund, Meredith R; Duffy, Joseph R; Strand, Edythe A; Machulda, Mary M; Whitwell, Jennifer L; Josephs, Keith A

2014-04-01

To determine how well the consensus criteria could classify subjects with primary progressive aphasia (PPA) using a quantitative speech and language battery that matches the test descriptions provided by the consensus criteria. A total of 105 participants with a neurodegenerative speech and language disorder were prospectively recruited and underwent neurologic, neuropsychological, and speech and language testing and MRI in this case-control study. Twenty-one participants with apraxia of speech without aphasia served as controls. Select tests from the speech and language battery were chosen for application of consensus criteria and cutoffs were employed to determine syndromic classification. Hierarchical cluster analysis was used to examine participants who could not be classified. Of the 84 participants, 58 (69%) could be classified as agrammatic (27%), semantic (7%), or logopenic (35%) variants of PPA. The remaining 31% of participants could not be classified. Of the unclassifiable participants, 2 clusters were identified. The speech and language profile of the first cluster resembled mild logopenic PPA and the second cluster semantic PPA. Gray matter patterns of loss of these 2 clusters of unclassified participants also resembled mild logopenic and semantic variants. Quantitative application of consensus PPA criteria yields the 3 syndromic variants but leaves a large proportion unclassified. Therefore, the current consensus criteria need to be modified in order to improve sensitivity.

Putting the pediatrics milestones into practice: a consensus roadmap and resource analysis.

PubMed

Schumacher, Daniel J; Spector, Nancy D; Calaman, Sharon; West, Daniel C; Cruz, Mario; Frohna, John G; Gonzalez Del Rey, Javier; Gustafson, Kristina K; Poynter, Sue Ellen; Rosenbluth, Glenn; Southgate, W Michael; Vinci, Robert J; Sectish, Theodore C

2014-05-01

The Accreditation Council for Graduate Medical Education has partnered with member boards of the American Board of Medical Specialties to initiate the next steps in advancing competency-based assessment in residency programs. This initiative, known as the Milestone Project, is a paradigm shift from traditional assessment efforts and requires all pediatrics residency programs to report individual resident progression along a series of 4 to 5 developmental levels of performance, or milestones, for individual competencies every 6 months beginning in June 2014. The effort required to successfully make this shift is tremendous given the number of training programs, training institutions, and trainees. However, it holds great promise for achieving training outcomes that align with patient needs; developing a valid, reliable, and meaningful way to track residents' development; and providing trainees with a roadmap for learning. Recognizing the resources needed to implement this new system, the authors, all residency program leaders, provide their consensus view of the components necessary for implementing and sustaining this effort, including resource estimates for completing this work. The authors have identified 4 domains: (1) Program Review and Development of Stakeholders and Participants, (2) Assessment Methods and Validation, (3) Data and Assessment System Development, and (4) Summative Assessment and Feedback. This work can serve as a starting point and framework for collaboration with program, department, and institutional leaders to identify and garner necessary resources and plan for local and national efforts that will ensure successful transition to milestones-based assessment. Copyright © 2014 by the American Academy of Pediatrics.

A Five-Country Survey on Ethics Education in Preservice Teaching Programs

ERIC Educational Resources Information Center

Maxwell, Bruce; Tremblay-Laprise, Audrée-Anne; Filion, Marianne; Boon, Helen; Daly, Caroline; van den Hoven, Mariette; Heilbronn, Ruth; Lenselink, Myrthe; Walters, Sue

2016-01-01

Despite a broad consensus on the ethical dimensions of the teaching profession, and long-standing efforts to align teacher education with wider trends in professional education, little is known about how teacher candidates are being prepared to face the ethical challenges of contemporary teaching. This article presents the results of an…

CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design

PubMed Central

Rose, Timothy M.; Henikoff, Jorja G.; Henikoff, Steven

2003-01-01

We have developed a new primer design strategy for PCR amplification of distantly related gene sequences based on consensus-degenerate hybrid oligonucleotide primers (CODEHOPs). An interactive program has been written to design CODEHOP PCR primers from conserved blocks of amino acids within multiply-aligned protein sequences. Each CODEHOP consists of a pool of related primers containing all possible nucleotide sequences encoding 3–4 highly conserved amino acids within a 3′ degenerate core. A longer 5′ non-degenerate clamp region contains the most probable nucleotide predicted for each flanking codon. CODEHOPs are used in PCR amplification to isolate distantly related sequences encoding the conserved amino acid sequence. The primer design software and the CODEHOP PCR strategy have been utilized for the identification and characterization of new gene orthologs and paralogs in different plant, animal and bacterial species. In addition, this approach has been successful in identifying new pathogen species. The CODEHOP designer (http://blocks.fhcrc.org/codehop.html) is linked to BlockMaker and the Multiple Alignment Processor within the Blocks Database World Wide Web (http://blocks.fhcrc.org). PMID:12824413

Supply-side options for an endgame for the tobacco industry.

PubMed

Callard, Cynthia D; Collishaw, Neil E

2013-05-01

Although governments have imposed controls on tobacco company behaviour, they have not yet aligned tobacco industry goals to public health objectives. As a result, tobacco companies have delayed or diminished the impact of imposed public health measures and have not contributed to curbing the epidemic of tobacco use. Over the past decade, several regulatory innovations have been proposed as ways to better align industry actions with public health needs, but none have been put in place. These policy suggestions share the goal of providing a supply-side complement to conventional demand reduction strategies, but they differ in the assumptions they make and in the regulatory and governance approaches they take. Similarly, differing views on ideology and political context within the tobacco control community and between governments may hinder the establishment of a global consensus on the ideal supply-side intervention. A government willing to implement innovative supply-side strategies as part of a tobacco control endgame may not require such consensus if factors specific to their national public health systems or political contexts are supportive.

Supply-side options for an endgame for the tobacco industry

PubMed Central

Callard, Cynthia D; Collishaw, Neil E

2013-01-01

Although governments have imposed controls on tobacco company behaviour, they have not yet aligned tobacco industry goals to public health objectives. As a result, tobacco companies have delayed or diminished the impact of imposed public health measures and have not contributed to curbing the epidemic of tobacco use. Over the past decade, several regulatory innovations have been proposed as ways to better align industry actions with public health needs, but none have been put in place. These policy suggestions share the goal of providing a supply-side complement to conventional demand reduction strategies, but they differ in the assumptions they make and in the regulatory and governance approaches they take. Similarly, differing views on ideology and political context within the tobacco control community and between governments may hinder the establishment of a global consensus on the ideal supply-side intervention. A government willing to implement innovative supply-side strategies as part of a tobacco control endgame may not require such consensus if factors specific to their national public health systems or political contexts are supportive. PMID:23591497

Monitoring Children with Reading Disabilities' Response to Phonics Intervention: Are There Differences between Intervention Aligned and General Skill Progress Monitoring Assessments?

ERIC Educational Resources Information Center

Olinghouse, Natalie G.; Lambert, Warren; Compton, Donald L.

2006-01-01

This study investigated whether 2 different progress monitoring assessments differentially predicted growth in reading skills associated with systematic phonics instruction. Oral reading fluency (ORE) was compared with an intervention aligned word list (IAWL) as predictors of growth in untimed and timed decoding and word identification and text…

Heterogeneous voter models

NASA Astrophysics Data System (ADS)

Masuda, Naoki; Gibert, N.; Redner, S.

2010-07-01

We introduce the heterogeneous voter model (HVM), in which each agent has its own intrinsic rate to change state, reflective of the heterogeneity of real people, and the partisan voter model (PVM), in which each agent has an innate and fixed preference for one of two possible opinion states. For the HVM, the time until consensus is reached is much longer than in the classic voter model. For the PVM in the mean-field limit, a population evolves to a preference-based state, where each agent tends to be aligned with its internal preference. For finite populations, discrete fluctuations ultimately lead to consensus being reached in a time that scales exponentially with population size.

A greedy, graph-based algorithm for the alignment of multiple homologous gene lists.

PubMed

Fostier, Jan; Proost, Sebastian; Dhoedt, Bart; Saeys, Yvan; Demeester, Piet; Van de Peer, Yves; Vandepoele, Klaas

2011-03-15

Many comparative genomics studies rely on the correct identification of homologous genomic regions using accurate alignment tools. In such case, the alphabet of the input sequences consists of complete genes, rather than nucleotides or amino acids. As optimal multiple sequence alignment is computationally impractical, a progressive alignment strategy is often employed. However, such an approach is susceptible to the propagation of alignment errors in early pairwise alignment steps, especially when dealing with strongly diverged genomic regions. In this article, we present a novel accurate and efficient greedy, graph-based algorithm for the alignment of multiple homologous genomic segments, represented as ordered gene lists. Based on provable properties of the graph structure, several heuristics are developed to resolve local alignment conflicts that occur due to gene duplication and/or rearrangement events on the different genomic segments. The performance of the algorithm is assessed by comparing the alignment results of homologous genomic segments in Arabidopsis thaliana to those obtained by using both a progressive alignment method and an earlier graph-based implementation. Especially for datasets that contain strongly diverged segments, the proposed method achieves a substantially higher alignment accuracy, and proves to be sufficiently fast for large datasets including a few dozens of eukaryotic genomes. http://bioinformatics.psb.ugent.be/software. The algorithm is implemented as a part of the i-ADHoRe 3.0 package.

B-cell Ligand Processing Pathways Detected by Large-scale Comparative Analysis

PubMed Central

Towfic, Fadi; Gupta, Shakti; Honavar, Vasant; Subramaniam, Shankar

2012-01-01

The initiation of B-cell ligand recognition is a critical step for the generation of an immune response against foreign bodies. We sought to identify the biochemical pathways involved in the B-cell ligand recognition cascade and sets of ligands that trigger similar immunological responses. We utilized several comparative approaches to analyze the gene coexpression networks generated from a set of microarray experiments spanning 33 different ligands. First, we compared the degree distributions of the generated networks. Second, we utilized a pairwise network alignment algorithm, BiNA, to align the networks based on the hubs in the networks. Third, we aligned the networks based on a set of KEGG pathways. We summarized our results by constructing a consensus hierarchy of pathways that are involved in B cell ligand recognition. The resulting pathways were further validated through literature for their common physiological responses. Collectively, the results based on our comparative analyses of degree distributions, alignment of hubs, and alignment based on KEGG pathways provide a basis for molecular characterization of the immune response states of B-cells and demonstrate the power of comparative approaches (e.g., gene coexpression network alignment algorithms) in elucidating biochemical pathways involved in complex signaling events in cells. PMID:22917187

Analyzing and synthesizing phylogenies using tree alignment graphs.

PubMed

Smith, Stephen A; Brown, Joseph W; Hinchliff, Cody E

2013-01-01

Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG). The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees), we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe.

Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs

PubMed Central

Smith, Stephen A.; Brown, Joseph W.; Hinchliff, Cody E.

2013-01-01

Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG). The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees), we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe. PMID:24086118

Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW.

PubMed

Oliver, Tim; Schmidt, Bertil; Nathan, Darran; Clemens, Ralf; Maskell, Douglas

2005-08-15

Aligning hundreds of sequences using progressive alignment tools such as ClustalW requires several hours on state-of-the-art workstations. We present a new approach to compute multiple sequence alignments in far shorter time using reconfigurable hardware. This results in an implementation of ClustalW with significant runtime savings on a standard off-the-shelf FPGA.

If Not Consensus, at Least Coherence and Transparency.

ERIC Educational Resources Information Center

Phillips, June K.

1995-01-01

Suggests that consensus is the result of intellectual inquiry among scholars for some common purpose. External and internal forces impel the academic community to move beyond argumentation about what students should be able to achieve as they progress. Legislatures and boards of regents are exercising increasing oversight over public and private…

Quantitative application of the primary progressive aphasia consensus criteria

PubMed Central

Wicklund, Meredith R.; Duffy, Joseph R.; Strand, Edythe A.; Machulda, Mary M.; Whitwell, Jennifer L.

2014-01-01

Objective: To determine how well the consensus criteria could classify subjects with primary progressive aphasia (PPA) using a quantitative speech and language battery that matches the test descriptions provided by the consensus criteria. Methods: A total of 105 participants with a neurodegenerative speech and language disorder were prospectively recruited and underwent neurologic, neuropsychological, and speech and language testing and MRI in this case-control study. Twenty-one participants with apraxia of speech without aphasia served as controls. Select tests from the speech and language battery were chosen for application of consensus criteria and cutoffs were employed to determine syndromic classification. Hierarchical cluster analysis was used to examine participants who could not be classified. Results: Of the 84 participants, 58 (69%) could be classified as agrammatic (27%), semantic (7%), or logopenic (35%) variants of PPA. The remaining 31% of participants could not be classified. Of the unclassifiable participants, 2 clusters were identified. The speech and language profile of the first cluster resembled mild logopenic PPA and the second cluster semantic PPA. Gray matter patterns of loss of these 2 clusters of unclassified participants also resembled mild logopenic and semantic variants. Conclusions: Quantitative application of consensus PPA criteria yields the 3 syndromic variants but leaves a large proportion unclassified. Therefore, the current consensus criteria need to be modified in order to improve sensitivity. PMID:24598709

Does the sagittal alignment of the cervical spine have an impact on disk degeneration? Minimum 10-year follow-up of asymptomatic volunteers

PubMed Central

Okada, Eijiro; Ichihara, Daisuke; Chiba, Kazuhiro; Toyama, Yoshiaki; Fujiwara, Hirokazu; Momoshima, Suketaka; Nishiwaki, Yuji; Hashimoto, Takeshi; Ogawa, Jun; Watanabe, Masahiko; Takahata, Takeshi

2009-01-01

There have been few studies that investigated and clarified the relationships between progression of degenerative changes and sagittal alignment of the cervical spine. The objective of the study was to longitudinally evaluate the relationships among progression of degenerative changes of the cervical spine with age, the development of clinical symptoms and sagittal alignment of the cervical spine in healthy subjects. Out of 497 symptom-free volunteers who underwent MRI and plain radiography of the cervical spine between 1994 and 1996, 113 subjects (45 males and 68 females) who responded to our contacts were enrolled. All subjects underwent another MRI at an average of 11.3 years after the initial study. Their mean age at the time of the initial imaging was 36.6 ± 14.5 years (11–65 years). The items evaluated on MRI were (1) decrease in signal intensity of the intervertebral disks, (2) posterior disk protrusion, and (3) disk space narrowing. Each item was evaluated using a numerical grading system. The subjects were divided into four groups according to the age and sagittal alignment of the cervical spine, i.e., subjects under or over the age of 40 years, and subjects with the lordosis or non-lordosis type of sagittal alignment of the cervical spine. During the 10-year period, progression of decrease in signal intensity of the disk, posterior disk protrusion, and disk space narrowing were recognized in 64.6, 65.5, and 28.3% of the subjects, respectively. Progression of posterior disk protrusion was significantly more frequent in subjects over 40 years of age with non-lordosis type of sagittal alignment. Logistic regression analysis revealed that stiff shoulder was closely correlated with females (P = 0.001), and that numbness of the upper extremity was closely correlated with age (P = 0.030) and male (P = 0.038). However, no significant correlation between the sagittal alignment of the cervical spine and clinical symptoms was detected. Sagittal alignment of the cervical spine had some impact on the progression of degenerative changes of the cervical spine with aging; however, it had no correlation with the occurrence of future clinical symptoms. PMID:19609784

Improved Thermostability of Clostridium thermocellum Endoglucanase Cel8A by Using Consensus-Guided Mutagenesis

PubMed Central

Anbar, Michael; Gul, Ozgur; Lamed, Raphael; Sezerman, Ugur O.

2012-01-01

The use of thermostable cellulases is advantageous for the breakdown of lignocellulosic biomass toward the commercial production of biofuels. Previously, we have demonstrated the engineering of an enhanced thermostable family 8 cellulosomal endoglucanase (EC 3.2.1.4), Cel8A, from Clostridium thermocellum, using random error-prone PCR and a combination of three beneficial mutations, dominated by an intriguing serine-to-glycine substitution (M. Anbar, R. Lamed, E. A. Bayer, ChemCatChem 2:997–1003, 2010). In the present study, we used a bioinformatics-based approach involving sequence alignment of homologous family 8 glycoside hydrolases to create a library of consensus mutations in which residues of the catalytic module are replaced at specific positions with the most prevalent amino acids in the family. One of the mutants (G283P) displayed a higher thermal stability than the wild-type enzyme. Introducing this mutation into the previously engineered Cel8A triple mutant resulted in an optimized enzyme, increasing the half-life of activity by 14-fold at 85°C. Remarkably, no loss of catalytic activity was observed compared to that of the wild-type endoglucanase. The structural changes were simulated by molecular dynamics analysis, and specific regions were identified that contributed to the observed thermostability. Intriguingly, most of the proteins used for sequence alignment in determining the consensus residues were derived from mesophilic bacteria, with optimal temperatures well below that of C. thermocellum Cel8A. PMID:22389377

Content and Alignment of State Writing Standards and Assessments as Predictors of Student Writing Achievement: An Analysis of 2007 National Assessment of Educational Progress Data

ERIC Educational Resources Information Center

Troia, Gary A.; Olinghouse, Natalie G.; Zhang, Mingcai; Wilson, Joshua; Stewart, Kelly A.; Mo, Ya; Hawkins, Lisa

2018-01-01

We examined the degree to which content of states' writing standards and assessments (using measures of content range, frequency, balance, and cognitive complexity) and their alignment were related to student writing achievement on the 2007 National Assessment of Educational Progress (NAEP), while controlling for student, school, and state…

Homologues of insulinase, a new superfamily of metalloendopeptidases.

PubMed Central

Rawlings, N D; Barrett, A J

1991-01-01

On the basis of a statistical analysis of an alignment of the amino acid sequences, a new superfamily of metalloendopeptidases is proposed, consisting of human insulinase, Escherichia coli protease III and mitochondrial processing endopeptidases from Saccharomyces and Neurospora. These enzymes do not contain the 'HEXXH' consensus sequence found in all previously recognized zinc metalloendopeptidases. PMID:2025223

A new structural framework for integrating replication protein A into DNA processing machinery

PubMed Central

Brosey, Chris A.; Yan, Chunli; Tsutakawa, Susan E.; Heller, William T.; Rambo, Robert P.; Tainer, John A.; Ivanov, Ivaylo; Chazin, Walter J.

2013-01-01

By coupling the protection and organization of single-stranded DNA (ssDNA) with recruitment and alignment of DNA processing factors, replication protein A (RPA) lies at the heart of dynamic multi-protein DNA processing machinery. Nevertheless, how RPA coordinates biochemical functions of its eight domains remains unknown. We examined the structural biochemistry of RPA’s DNA-binding activity, combining small-angle X-ray and neutron scattering with all-atom molecular dynamics simulations to investigate the architecture of RPA’s DNA-binding core. The scattering data reveal compaction promoted by DNA binding; DNA-free RPA exists in an ensemble of states with inter-domain mobility and becomes progressively more condensed and less dynamic on binding ssDNA. Our results contrast with previous models proposing RPA initially binds ssDNA in a condensed state and becomes more extended as it fully engages the substrate. Moreover, the consensus view that RPA engages ssDNA in initial, intermediate and final stages conflicts with our data revealing that RPA undergoes two (not three) transitions as it binds ssDNA with no evidence for a discrete intermediate state. These results form a framework for understanding how RPA integrates the ssDNA substrate into DNA processing machinery, provides substrate access to its binding partners and promotes the progression and selection of DNA processing pathways. PMID:23303776

A new structural framework for integrating replication protein A into DNA processing machinery

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

Brosey, Chris; Yan, Chunli; Tsutakawa, Susan

2013-01-17

By coupling the protection and organization of single-stranded DNA (ssDNA) with recruitment and alignment of DNA processing factors, replication protein A (RPA) lies at the heart of dynamic multi-protein DNA processing machinery. Nevertheless, how RPA coordinates biochemical functions of its eight domains remains unknown. We examined the structural biochemistry of RPA's DNA-binding activity, combining small-angle X-ray and neutron scattering with all-atom molecular dynamics simulations to investigate the architecture of RPA's DNA-binding core. The scattering data reveal compaction promoted by DNA binding; DNA-free RPA exists in an ensemble of states with inter-domain mobility and becomes progressively more condensed and less dynamicmore » on binding ssDNA. Our results contrast with previous models proposing RPA initially binds ssDNA in a condensed state and becomes more extended as it fully engages the substrate. Moreover, the consensus view that RPA engages ssDNA in initial, intermediate and final stages conflicts with our data revealing that RPA undergoes two (not three) transitions as it binds ssDNA with no evidence for a discrete intermediate state. These results form a framework for understanding how RPA integrates the ssDNA substrate into DNA processing machinery, provides substrate access to its binding partners and promotes the progression and selection of DNA processing pathways.« less

Bioinformatics prediction of siRNAs as potential antiviral agents against dengue viruses

PubMed Central

Villegas-Rosales, Paula M; Méndez-Tenorio, Alfonso; Ortega-Soto, Elizabeth; Barrón, Blanca L

2012-01-01

Dengue virus (DENV 1-4) represents the major emerging arthropod-borne viral infection in the world. Currently, there is neither an available vaccine nor a specific treatment. Hence, there is a need of antiviral drugs for these viral infections; we describe the prediction of short interfering RNA (siRNA) as potential therapeutic agents against the four DENV serotypes. Our strategy was to carry out a series of multiple alignments using ClustalX program to find conserved sequences among the four DENV serotype genomes to obtain a consensus sequence for siRNAs design. A highly conserved sequence among the four DENV serotypes, located in the encoding sequence for NS4B and NS5 proteins was found. A total of 2,893 complete DENV genomes were downloaded from the NCBI, and after a depuration procedure to identify identical sequences, 220 complete DENV genomes were left. They were edited to select the NS4B and NS5 sequences, which were aligned to obtain a consensus sequence. Three different servers were used for siRNA design, and the resulting siRNAs were aligned to identify the most prevalent sequences. Three siRNAs were chosen, one targeted the genome region that codifies for NS4B protein and the other two; the region for NS5 protein. Predicted secondary structure for DENV genomes was used to demonstrate that the siRNAs were able to target the viral genome forming double stranded structures, necessary to activate the RNA silencing machinery. PMID:22829722

TU-C-12A-02: Development of a Multiparametric Statistical Response Map for Quantitative Imaging

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

Bosca, R; The University of Texas MD Anderson Cancer Center, Houston, TX; Mahajan, A

2014-06-15

Purpose: Quantitative imaging biomarkers (QIB) are becoming increasingly utilized in early phase clinical trials as a means of non-invasively assessing treatment response and associated response heterogeneity. The aim of this study was to develop a flexible multiparametric statistical framework to predict voxel-by-voxel response of several potential MRI QIBs. Methods: Patients with histologically proven glioblastomas (n=11) were treated with chemoradiation (with/without bevacizumab) and underwent one baseline and two mid-treatment (3–4wks) MRIs. Dynamic contrast-enhanced (3D FSPGR, 6.3sec/phase, 0.1 mmol/kg Gd-DTPA), dynamic susceptibility contrast (2D GRE-EPI, 1.5sec/phase, 0.2mmol/kg Gd-DTPA), and diffusion tensor (2D DW-EPI, b=0, 1200 s/mm{sup 2}, 27 directions) imaging acquisitions weremore » obtained during each study. Mid-treatment and pre-treatment images were rigidly aligned, and regions of partial response (PR), stable disease (SD), and progressive disease (PD) were contoured in consensus by two experienced radiation oncologists. Voxels in these categories were used to train ordinal (PR« less

Aligning Science Assessment Standards: Oklahoma and the 2009 National Assessment of Educational Progress (NAEP). Issues & Answers. REL 2007-No. 022

ERIC Educational Resources Information Center

Timms, Michael; Schneider, Steven; Lee, Cindy; Rolfhus, Eric

2007-01-01

This policy research document is intended for Oklahoma policymakers to use when examining possible changes to the state assessment's alignment with the National Assessment of Educational Progress (NAEP). The 2009 NAEP test is not yet in existence, so the purpose of this report is to give policymakers a head start in determining where they might,…

MANGO: a new approach to multiple sequence alignment.

PubMed

Zhang, Zefeng; Lin, Hao; Li, Ming

2007-01-01

Multiple sequence alignment is a classical and challenging task for biological sequence analysis. The problem is NP-hard. The full dynamic programming takes too much time. The progressive alignment heuristics adopted by most state of the art multiple sequence alignment programs suffer from the 'once a gap, always a gap' phenomenon. Is there a radically new way to do multiple sequence alignment? This paper introduces a novel and orthogonal multiple sequence alignment method, using multiple optimized spaced seeds and new algorithms to handle these seeds efficiently. Our new algorithm processes information of all sequences as a whole, avoiding problems caused by the popular progressive approaches. Because the optimized spaced seeds are provably significantly more sensitive than the consecutive k-mers, the new approach promises to be more accurate and reliable. To validate our new approach, we have implemented MANGO: Multiple Alignment with N Gapped Oligos. Experiments were carried out on large 16S RNA benchmarks showing that MANGO compares favorably, in both accuracy and speed, against state-of-art multiple sequence alignment methods, including ClustalW 1.83, MUSCLE 3.6, MAFFT 5.861, Prob-ConsRNA 1.11, Dialign 2.2.1, DIALIGN-T 0.2.1, T-Coffee 4.85, POA 2.0 and Kalign 2.0.

Articular chondrocyte alignment in the rat after surgically induced osteoarthritis

PubMed Central

Takahashi, Hideaki; Tamaki, Hiroyuki; Yamamoto, Noriaki; Onishi, Hideaki

2017-01-01

[Purpose] Chondrocytes in articular cartilage are aligned as columns from the joint surface. Notably, loss of chondrocyte and abnormalities of differentiation factors give rise to osteoarthritis (OA). However, the relationship between chondrocyte alignment and OA progression remains unclear. This study was performed to investigate temporal alterations in surgically-induced OA rats. [Subjects and Methods] Thirteen-week-old Wistar rats (n=30) underwent destabilized medial meniscus surgery in their right knee and sham surgery in their left knee. Specimens (n=5) were collected at 0, 1, 2, 4 and 8 weeks after surgery. Histological analysis with Osteoarthritis Research Society International (OARSI) scores, cell density ratios, cell alignments and correlation between OARSI scores and cell density/alignment was performed. [Results] OARSI scores were significantly higher at 1, 2, 4 and 8 weeks in the DMM group than in the control. Cell density ratios were decreased significantly in the DMM group at 2, 4 and 8 weeks compared with the control. Chondrocyte alignment was decreased significantly in the DMM group at 4 and 8 weeks. There were negative correlations between OA severity and cell density / cell alignment. [Conclusion] The results suggest a relationship between chondrocyte alignment and cartilage homeostasis, which plays an important role in OA progression. PMID:28533592

Flocking dynamics with voter-like interactions

NASA Astrophysics Data System (ADS)

Baglietto, Gabriel; Vazquez, Federico

2018-03-01

We study the collective motion of a large set of self-propelled particles subject to voter-like interactions. Each particle moves on a 2D space at a constant speed in a direction that is randomly assigned initially. Then, at every step of the dynamics, each particle adopts the direction of motion of a randomly chosen neighboring particle. We investigate the time evolution of the global alignment of particles measured by the order parameter φ, until complete order \\varphi=1.0 is reached (polar consensus). We find that φ increases as t 1/2 for short times and approaches 1.0 exponentially fast for longer times. Also, the mean time to consensus τ varies non-monotonically with the density of particles ρ, reaching a minimum at some intermediate density ρmin . At ρmin , the mean consensus time scales with the system size N as τmin ∼ N0.765 , and thus the consensus is faster than in the case of all-to-all interactions (large ρ) where τ=2N . We show that the fast consensus, also observed at intermediate and high densities, is a consequence of the segregation of the system into clusters of equally-oriented particles which breaks the balance of transitions between directional states in well mixed systems.

Harmonising data collection from osteoarthritis studies to enable stratification: recommendations on core data collection from an Arthritis Research UK clinical studies group

PubMed Central

Corp, Nadia; Watt, Fiona E.; Felson, David T.; O’Neill, Terence W.; Holt, Cathy A.; Jones, Richard K.; Conaghan, Philip G.; Arden, Nigel K.

2016-01-01

Objective. Treatment of OA by stratifying for commonly used and novel therapies will likely improve the range of effective therapy options and their rational deployment in this undertreated, chronic disease. In order to develop appropriate datasets for conducting post hoc analyses to inform approaches to stratification for OA, our aim was to develop recommendations on the minimum data that should be recorded at baseline in all future OA interventional and observational studies. Methods. An Arthritis Research UK study group comprised of 32 experts used a Delphi-style approach supported by a literature review of systematic reviews to come to a consensus on core data collection for OA studies. Results. Thirty-five systematic reviews were used as the basis for the consensus group discussion. For studies with a primary structural endpoint, core domains for collection were defined as BMI, age, gender, racial origin, comorbidities, baseline OA pain, pain in other joints and occupation. In addition to the items generalizable to all anatomical sites, joint-specific domains included radiographic measures, surgical history and anatomical factors, including alignment. To demonstrate clinical relevance for symptom studies, the collection of mental health score, self-efficacy and depression scales were advised in addition to the above. Conclusions. Currently it is not possible to stratify patients with OA into therapeutic groups. A list of core and optional data to be collected in all OA interventional and observational studies was developed, providing a basis for future analyses to identify predictors of progression or response to treatment. PMID:27084310

Views of Old Forestry and New Among Reference Groups in the Pacific Northwest

Treesearch

Robert G. Ribe; Mollie Y. Matteson

2002-01-01

A public opinion survey was conducted in Washington and Oregon. It was not a representative poll sample but instead sampled groups of people favoring forest production, those favaring forest protection, and others not aligned with either of these viewpoints. There is strong consensus across groups regarding the unpopularity of established forestry methods and the need...

Analysis of Ribosome Inactivating Protein (RIP): A Bioinformatics Approach

NASA Astrophysics Data System (ADS)

Jothi, G. Edward Gnana; Majilla, G. Sahaya Jose; Subhashini, D.; Deivasigamani, B.

2012-10-01

In spite of the medical advances in recent years, the world is in need of different sources to encounter certain health issues.Ribosome Inactivating Proteins (RIPs) were found to be one among them. In order to get easy access about RIPs, there is a need to analyse RIPs towards constructing a database on RIPs. Also, multiple sequence alignment was done towards screening for homologues of significant RIPs from rare sources against RIPs from easily available sources in terms of similarity. Protein sequences were retrieved from SWISS-PROT and are further analysed using pair wise and multiple sequence alignment.Analysis shows that, 151 RIPs have been characterized to date. Amongst them, there are 87 type I, 37 type II, 1 type III and 25 unknown RIPs. The sequence length information of various RIPs about the availability of full or partial sequence was also found. The multiple sequence alignment of 37 type I RIP using the online server Multalin, indicates the presence of 20 conserved residues. Pairwise alignment and multiple sequence alignment of certain selected RIPs in two groups namely Group I and Group II were carried out and the consensus level was found to be 98%, 98% and 90% respectively.

Building Consensus for Change: Developing an Administrative and Management Structure in a Southern African University.

ERIC Educational Resources Information Center

Ingalls, Wayne B.

1995-01-01

The way in which the University of Botswana went about building the consensus necessary to develop a new administrative and management structure is described. The process began with a commission review to address increasing demand, and progressed to recommendations, governing council response, a task force for reorganization, and implementation.…

Collaboratively managing sudden oak death using tangible geospatial modeling

Treesearch

Ross K. Meentemeyer; Francesco Tonini; Douglas Shoemaker; Richard C. Cobb; Brendan A. Harmon; Vaclav Petras; Anna Petrasova; Helena Mitasova

2017-01-01

Failure to build consensus amongst stakeholders has been a primary obstacle barring progress in developing and implementing strategies to manage sudden oak death (SOD). Consensus as to the goals of in situ management of SOD has rarely been reached, because stakeholders’ visions of success vary widely and often compete with each other...

Predicting reading outcomes with progress monitoring slopes among middle grade students

PubMed Central

Tolar, Tammy D.; Barth, Amy E.; Fletcher, Jack M.; Francis, David J.; Vaughn, Sharon

2013-01-01

Effective implementation of response-to-intervention (RTI) frameworks depends on efficient tools for monitoring progress. Evaluations of growth (i.e., slope) may be less efficient than evaluations of status at a single time point, especially if slopes do not add to predictions of outcomes over status. We examined progress monitoring slope validity for predicting reading outcomes among middle school students by evaluating latent growth models for different progress monitoring measure-outcome combinations. We used multi-group modeling to evaluate the effects of reading ability, reading intervention, and progress monitoring administration condition on slope validity. Slope validity was greatest when progress monitoring was aligned with the outcome (i.e., word reading fluency slope was used to predict fluency outcomes in contrast to comprehension outcomes), but effects varied across administration conditions (viz., repeated reading of familiar vs. novel passages). Unless the progress monitoring measure is highly aligned with outcome, slope may be an inefficient method for evaluating progress in an RTI context. PMID:24659899

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

Wang, Wei; Liu, Yang; Zu, Xiangyang

Highlights: {yields} Successfully selected specific PreS1-interacting peptides by using phage displayed library. {yields} Alignment of the positive phage clones revealed a consensus PreS1 binding motif. {yields} A highly enriched peptide named P7 had a strong binding ability for PreS1. {yields} P7 could block PreS1 attachment. -- Abstract: The PreS1 protein is present on the outermost part of the hepatitis B virus (HBV) surface and has been shown to have a pivotal function in viral infectivity and assembly. The development of reagents with high affinity and specificity for PreS1 is of great significance for early diagnosis and treatment of HBV infection.more » A phage display library of dodecapeptide was screened for interactions with purified PreS1 protein. Alignment of the positive phage clones revealed a putative consensus PreS1 binding motif of HX{sub n}HX{sub m}HP/R. Moreover, a peptide named P7 (KHMHWHPPALNT) was highly enriched and occurred with a surprisingly high frequency of 72%. A thermodynamic study revealed that P7 has a higher binding affinity to PreS1 than the other peptides. Furthermore, P7 was able to abrogate the binding of HBV virions to the PreS1 antibody, suggesting that P7 covers key functional sites on the native PreS1 protein. This newly isolated peptide may, therefore, be a new therapeutic candidate for the treatment of HBV. The consensus motif could be modified to deliver imaging, diagnostic, and therapeutic agents to tissues affected by HBV.« less

Consensus Paper: Pathological Mechanisms Underlying Neurodegeneration in Spinocerebellar Ataxias

PubMed Central

Matilla-Dueñas, A.; Ashizawa, T.; Brice, A.; Magri, S.; McFarland, K. N.; Pandolfo, M.; Pulst, S. M.; Riess, O.; Rubinsztein, D. C.; Schmidt, J.; Schmidt, T.; Scoles, D. R.; Stevanin, G.; Taroni, F.; Underwood, B. R.; Sánchez, I.

2014-01-01

Intensive scientific research devoted in the recent years to understand the molecular mechanisms or neurodegeneration in spinocerebellar ataxias (SCAs) are identifying new pathways and targets providing new insights and a better understanding of the molecular pathogenesis in these diseases. In this consensus manuscript, the authors discuss their current views on the identified molecular processes causing or modulating the neurodegenerative phenotype in spinocerebellar ataxias with the common opinion of translating the new knowledge acquired into candidate targets for therapy. The following topics are discussed: transcription dysregulation, protein aggregation, autophagy, ion channels, the role of mitochondria, RNA toxicity, modulators of neurodegeneration and current therapeutic approaches. Overall point of consensus includes the common vision of neurodegeneration in SCAs as a multifactorial, progressive and reversible process, at least in early stages. Specific points of consensus include the role of the dysregulation of protein folding, transcription, bioenergetics, calcium handling and eventual cell death with apoptotic features of neurons during SCA disease progression. Unresolved questions include how the dysregulation of these pathways triggers the onset of symptoms and mediates disease progression since this understanding may allow effective treatments of SCAs within the window of reversibility to prevent early neuronal damage. Common opinions also include the need for clinical detection of early neuronal dysfunction, for more basic research to decipher the early neurodegenerative process in SCAs in order to give rise to new concepts for treatment strategies and for the translation of the results to preclinical studies and, thereafter, in clinical practice. PMID:24307138

Tibiofemoral Osteoarthritis and Varus-Valgus Laxity

PubMed Central

Freisinger, Gregory M.; Schmitt, Laura C.; Wanamaker, Andrea B.; Siston, Robert A.; Chaudhari, Ajit M. W.

2017-01-01

The purpose of this study was to systematically review and synthesize the literature measuring varus-valgus laxity in individuals with tibiofemoral osteoarthritis (OA). Specifically, we aimed to identify varus-valgus laxity differences between persons with OA and controls, by radiographic disease severity, by frontal plane knee alignment, and by sex. We also aimed to identify if there was a relationship between varus-valgus laxity and clinical performance and self-reported function. We systematically searched for peer-reviewed original research articles in PubMed, Scopus, and CINAHL to identify all existing literature regarding knee OA and objective measurement of varus-valgus laxity in vivo. Forty articles were identified that met the inclusion criteria and data were extracted. Varus-valgus laxity was significantly greater in individuals with OA compared with controls in a majority of studies, while no study found laxity to be significantly greater in controls. Varus-valgus laxity of the knee was reported in persons with OA and varying degrees of frontal plane alignment, disease severity, clinical performance, and self-reported function but no consensus finding could be identified. Females with knee OA appear to have more varus-valgus laxity than males. Meta-analysis was not possible due to the heterogeneity of the subject populations and differences in laxity measurement devices, applied loading, and laxity definitions. Increased varus-valgus laxity is a characteristic of knee joints with OA. Large variances exist in reported varus-valgus laxity and may be due to differences in measurement devices. Prospective studies on joint laxity are needed to identify if increased varus-valgus laxity is a causative factor in OA incidence and progression. PMID:27680888

A portable foot-parameter-extracting system

NASA Astrophysics Data System (ADS)

Zhang, MingKai; Liang, Jin; Li, Wenpan; Liu, Shifan

2016-03-01

In order to solve the problem of automatic foot measurement in garment customization, a new automatic footparameter- extracting system based on stereo vision, photogrammetry and heterodyne multiple frequency phase shift technology is proposed and implemented. The key technologies applied in the system are studied, including calibration of projector, alignment of point clouds, and foot measurement. Firstly, a new projector calibration algorithm based on plane model has been put forward to get the initial calibration parameters and a feature point detection scheme of calibration board image is developed. Then, an almost perfect match of two clouds is achieved by performing a first alignment using the Sampled Consensus - Initial Alignment algorithm (SAC-IA) and refining the alignment using the Iterative Closest Point algorithm (ICP). Finally, the approaches used for foot-parameterextracting and the system scheme are presented in detail. Experimental results show that the RMS error of the calibration result is 0.03 pixel and the foot parameter extracting experiment shows the feasibility of the extracting algorithm. Compared with the traditional measurement method, the system can be more portable, accurate and robust.

The Alignment of easyCBM[R] Math Measures to Curriculum Standards. Technical Report #1002

ERIC Educational Resources Information Center

Nese, Joseph F. T.; Lai, Cheng-Fei; Anderson, Daniel; Park, Bitnara Jasmine; Tindal, Gerald; Alonzo, Julie

2010-01-01

The purpose of this study was to examine the alignment of the easyCBM[R] mathematics benchmark and progress monitoring measures to the National Council of Teachers of Mathematics "Curriculum Focal Points" (NCTM, 2006). Based on Webb's alignment model (1997, 2002), we collected expert judgments on individual math items across a sampling of forms…

The fractured landscape of RNA-seq alignment: the default in our STARs.

PubMed

Ballouz, Sara; Dobin, Alexander; Gingeras, Thomas R; Gillis, Jesse

2018-06-01

Many tools are available for RNA-seq alignment and expression quantification, with comparative value being hard to establish. Benchmarking assessments often highlight methods' good performance, but are focused on either model data or fail to explain variation in performance. This leaves us to ask, what is the most meaningful way to assess different alignment choices? And importantly, where is there room for progress? In this work, we explore the answers to these two questions by performing an exhaustive assessment of the STAR aligner. We assess STAR's performance across a range of alignment parameters using common metrics, and then on biologically focused tasks. We find technical metrics such as fraction mapping or expression profile correlation to be uninformative, capturing properties unlikely to have any role in biological discovery. Surprisingly, we find that changes in alignment parameters within a wide range have little impact on both technical and biological performance. Yet, when performance finally does break, it happens in difficult regions, such as X-Y paralogs and MHC genes. We believe improved reporting by developers will help establish where results are likely to be robust or fragile, providing a better baseline to establish where methodological progress can still occur.

Infant-Mother Acoustic-Prosodic Alignment and Developmental Risk.

PubMed

Seidl, Amanda; Cristia, Alejandrina; Soderstrom, Melanie; Ko, Eon-Suk; Abel, Emily A; Kellerman, Ashleigh; Schwichtenberg, A J

2018-06-19

One promising early marker for autism and other communicative and language disorders is early infant speech production. Here we used daylong recordings of high- and low-risk infant-mother dyads to examine whether acoustic-prosodic alignment as well as two automated measures of infant vocalization are related to developmental risk status indexed via familial risk and developmental progress at 36 months of age. Automated analyses of the acoustics of daylong real-world interactions were used to examine whether pitch characteristics of one vocalization by the mother or the child predicted those of the vocalization response by the other speaker and whether other features of infants' speech in daylong recordings were associated with developmental risk status or outcomes. Low-risk and high-risk dyads did not differ in the level of acoustic-prosodic alignment, which was overall not significant. Further analyses revealed that acoustic-prosodic alignment did not predict infants' later developmental progress, which was, however, associated with two automated measures of infant vocalizations (daily vocalizations and conversational turns). Although further research is needed, these findings suggest that automated measures of vocalizations drawn from daylong recordings are a possible early identification tool for later developmental progress/concerns. https://osf.io/cdn3v/.

Aligning interprofessional education collaborative sub-competencies to a progression of learning.

PubMed

Patel Gunaldo, Tina; Brisolara, Kari Fitzmorris; Davis, Alison H; Moore, Robert

2017-05-01

In the United States, the Interprofessional Education Collaborative (IPEC) developed four core competencies for interprofessional collaborative practice. Even though the IPEC competencies and respective sub-competencies were not created in a hierarchal manner, one might reflect upon a logical progression of learning as well as learners accruing skills allowing them to master one level of learning and building on the aggregate of skills before advancing to the next level. The Louisiana State University Health-New Orleans Center for Interprofessional Education and Collaborative Practice (CIPECP) determined the need to align the sub-competencies with the level of behavioural expectations in order to simplify the process of developing an interprofessional education experience targeted to specific learning levels. In order to determine the most effective alignment, CIPECP discussions revolved around current programmatic expectations across the institution. Faculty recognised the need to align sub-competencies with student learning objectives. Simultaneously, a progression of learning existing within each of the four IPEC domains was noted. Ultimately, the faculty and staff team agreed upon categorising the sub-competencies in a hierarchical manner for the four domains into either a "basic, intermediate, or advanced" level of competency.

Connective Tissue Disease-associated Interstitial Lung Diseases (CTD-ILD) - Report from OMERACT CTD-ILD Working Group.

PubMed

Khanna, Dinesh; Mittoo, Shikha; Aggarwal, Rohit; Proudman, Susanna M; Dalbeth, Nicola; Matteson, Eric L; Brown, Kevin; Flaherty, Kevin; Wells, Athol U; Seibold, James R; Strand, Vibeke

2015-11-01

Interstitial lung disease (ILD) is common in connective tissue disease (CTD) and is the leading cause of mortality. Investigators have used certain outcome measures in randomized controlled trials (RCT) in CTD-ILD, but the lack of a systematically developed, CTD-specific index that captures all measures relevant and meaningful to patients with CTD-ILD has left a large and conspicuous gap in CTD-ILD research. The CTD-ILD working group, under the aegis of the Outcome Measures in Rheumatology (OMERACT) initiative, has completed a consensus group exercise to reach harmony on core domains and items for inclusion in RCT in CTD-ILD. During the OMERACT 12 meeting, consensus was sought on domains and core items for inclusion in RCT. In addition, consensus was pursued on a definition of response in RCT. Consensus was defined as ≥ 75% agreement among the participants. OMERACT 12 participants endorsed the domains with minimal modifications. Clinically meaningful progression for CTD-ILD was proposed as ≥ 10% relative decline in forced vital capacity (FVC) or ≥ 5% to < 10% relative decline in FVC and ≥ 15% relative decline in DLCO. There is consensus on domains for inclusion in RCT in CTD-ILD and on a definition of clinically meaningful progression. Data-driven approaches to validate these results in different cohorts and RCT are needed.

Applications for detection of acute kidney injury using electronic medical records and clinical information systems: workgroup statements from the 15(th) ADQI Consensus Conference.

PubMed

James, Matthew T; Hobson, Charles E; Darmon, Michael; Mohan, Sumit; Hudson, Darren; Goldstein, Stuart L; Ronco, Claudio; Kellum, John A; Bagshaw, Sean M

2016-01-01

Electronic medical records and clinical information systems are increasingly used in hospitals and can be leveraged to improve recognition and care for acute kidney injury. This Acute Dialysis Quality Initiative (ADQI) workgroup was convened to develop consensus around principles for the design of automated AKI detection systems to produce real-time AKI alerts using electronic systems. AKI alerts were recognized by the workgroup as an opportunity to prompt earlier clinical evaluation, further testing and ultimately intervention, rather than as a diagnostic label. Workgroup members agreed with designing AKI alert systems to align with the existing KDIGO classification system, but recommended future work to further refine the appropriateness of AKI alerts and to link these alerts to actionable recommendations for AKI care. The consensus statements developed in this review can be used as a roadmap for development of future electronic applications for automated detection and reporting of AKI.

Special Education Teacher Evaluation: Why It Matters, What Makes It Challenging, and How to Address These Challenges

ERIC Educational Resources Information Center

Johnson, Evelyn; Semmelroth, Carrie Lisa

2014-01-01

There is currently little consensus on how special education teachers should be evaluated. The lack of consensus may be due to several reasons. Special education teachers work under a variety of complex conditions, with a very heterogeneous population, and support student progress toward a very individualized set of goals. In addition, special…

Valorisation of urban elements through 3D models generated from image matching point clouds and augmented reality visualization based in mobile platforms

NASA Astrophysics Data System (ADS)

Marques, Luís.; Roca Cladera, Josep; Tenedório, José António

2017-10-01

The use of multiple sets of images with high level of overlapping to extract 3D point clouds has increased progressively in recent years. There are two main fundamental factors in the origin of this progress. In first, the image matching algorithms has been optimised and the software available that supports the progress of these techniques has been constantly developed. In second, because of the emergent paradigm of smart cities which has been promoting the virtualization of urban spaces and their elements. The creation of 3D models for urban elements is extremely relevant for urbanists to constitute digital archives of urban elements and being especially useful for enrich maps and databases or reconstruct and analyse objects/areas through time, building and recreating scenarios and implementing intuitive methods of interaction. These characteristics assist, for example, higher public participation creating a completely collaborative solution system, envisioning processes, simulations and results. This paper is organized in two main topics. The first deals with technical data modelling obtained by terrestrial photographs: planning criteria for obtaining photographs, approving or rejecting photos based on their quality, editing photos, creating masks, aligning photos, generating tie points, extracting point clouds, generating meshes, building textures and exporting results. The application of these procedures results in 3D models for the visualization of urban elements of the city of Barcelona. The second concerns the use of Augmented Reality through mobile platforms allowing to understand the city origins and the relation with the actual city morphology, (en)visioning solutions, processes and simulations, making possible for the agents in several domains, to fundament their decisions (and understand them) achieving a faster and wider consensus.

Surgery in ovarian cancer - Brazilian Society of Surgical Oncology consensus.

PubMed

Tsunoda, Audrey Tieko; Ribeiro, Reitan; Reis, Rosilene Jara; Andrade, Carlos Eduardo Mattos da Cunha; Marques, Renato Moretti; Baiocchi, Glauco; Fin, Fabio; Zanvettor, Paulo Henrique; Falcao, Deraldo; Batista, Thales Paulo; Azevedo, Bruno Roberto Braga; Guitmann, Gustavo; Pessini, Suzana Arenhart; Nunes, João Soares; Campbell, Leonardo Martins; Linhares, José Clemente; Coimbra, Felipe José Fernandez

2018-06-14

Surgical management in epithelial ovarian cancer (EOC) has a significant impact in overall survival (OS) and progression free survival (PFS). Brazilian Society of Surgical Oncology (BSSO) supported a taskforce with experts for consensus: experienced and specialized trained surgeons, in cancer centers, provide the best EOC surgery. Laparoscopic and/or radiological staging prognosticate the possibility of complete cytoreduction (CC0) and help to reduce unnecessary laparotomies. Surgical techniques were reviewed. Multidisciplinary input is essential for treatment planning. Quality assurance criteria are proposed and need national consensus. Genetic testing is mandatory. This consensus states the final recommendations from BSSO for management of EOC. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Assessment of Suicidal Ideation and Behavior: Report of the International Society for CNS Clinical Trials and Methodology Consensus Meeting.

PubMed

Chappell, Phillip B; Stewart, Michelle; Alphs, Larry; DiCesare, Franco; DuBrava, Sarah; Harkavy-Friedman, Jill; Lim, Pilar; Ratcliffe, Sian; Silverman, Morton M; Targum, Steven D; Marder, Stephen R

2017-06-01

To develop consensus recommendations for assessment of suicidal ideation/suicidal behavior (SI/SB) in clinical trials. Stakeholders from academia, industry, regulatory agencies, National Institutes of Health, National Institute of Mental Health, and patient advocacy organizations participated in a consensus meeting that was sponsored by the International Society for CNS Clinical Trials and Methodology and held November 17-18, 2015. Prior to the meeting, teams of experts identified key areas of consensus and dissent related to SI/SB. The most critical issues were presented and discussed in the consensus meeting. Literature reviews and a pre-meeting survey were conducted. Findings were discussed in pre-meeting working group sessions and at the consensus meeting. Five pre-meeting working groups reviewed (1) nomenclature and classification schemes for SI/SB, (2) detection and assessment of SI/SB, (3) analysis of SI/SB data, (4) design of clinical trials for new treatments of SI/SB, and (5) public health approaches to SI/SB. A modification of the RAND/UCLA Appropriateness Method was used to combine review of scientific evidence with the collective views of experts and stakeholders to reach the final consensus statements. After discussion, all attendees voted using an electronic interactive audience response system. Areas of agreement and areas of continuing dissent were recorded. All 5 working groups agreed that a major barrier to advancement of the field of SI/SB research and the development of new treatments for SI/SB remains the lack of a universally accepted standardized nomenclature and classification system. Achieving alignment on definitions and classification of suicide-related phenomena is critical to improving the detection and assessment of SI/SB, the design of clinical trials for new treatments, and effective public health interventions. © Copyright 2017 Physicians Postgraduate Press, Inc.

Mango: multiple alignment with N gapped oligos.

PubMed

Zhang, Zefeng; Lin, Hao; Li, Ming

2008-06-01

Multiple sequence alignment is a classical and challenging task. The problem is NP-hard. The full dynamic programming takes too much time. The progressive alignment heuristics adopted by most state-of-the-art works suffer from the "once a gap, always a gap" phenomenon. Is there a radically new way to do multiple sequence alignment? In this paper, we introduce a novel and orthogonal multiple sequence alignment method, using both multiple optimized spaced seeds and new algorithms to handle these seeds efficiently. Our new algorithm processes information of all sequences as a whole and tries to build the alignment vertically, avoiding problems caused by the popular progressive approaches. Because the optimized spaced seeds have proved significantly more sensitive than the consecutive k-mers, the new approach promises to be more accurate and reliable. To validate our new approach, we have implemented MANGO: Multiple Alignment with N Gapped Oligos. Experiments were carried out on large 16S RNA benchmarks, showing that MANGO compares favorably, in both accuracy and speed, against state-of-the-art multiple sequence alignment methods, including ClustalW 1.83, MUSCLE 3.6, MAFFT 5.861, ProbConsRNA 1.11, Dialign 2.2.1, DIALIGN-T 0.2.1, T-Coffee 4.85, POA 2.0, and Kalign 2.0. We have further demonstrated the scalability of MANGO on very large datasets of repeat elements. MANGO can be downloaded at http://www.bioinfo.org.cn/mango/ and is free for academic usage.

enoLOGOS: a versatile web tool for energy normalized sequence logos

PubMed Central

Workman, Christopher T.; Yin, Yutong; Corcoran, David L.; Ideker, Trey; Stormo, Gary D.; Benos, Panayiotis V.

2005-01-01

enoLOGOS is a web-based tool that generates sequence logos from various input sources. Sequence logos have become a popular way to graphically represent DNA and amino acid sequence patterns from a set of aligned sequences. Each position of the alignment is represented by a column of stacked symbols with its total height reflecting the information content in this position. Currently, the available web servers are able to create logo images from a set of aligned sequences, but none of them generates weighted sequence logos directly from energy measurements or other sources. With the advent of high-throughput technologies for estimating the contact energy of different DNA sequences, tools that can create logos directly from binding affinity data are useful to researchers. enoLOGOS generates sequence logos from a variety of input data, including energy measurements, probability matrices, alignment matrices, count matrices and aligned sequences. Furthermore, enoLOGOS can represent the mutual information of different positions of the consensus sequence, a unique feature of this tool. Another web interface for our software, C2H2-enoLOGOS, generates logos for the DNA-binding preferences of the C2H2 zinc-finger transcription factor family members. enoLOGOS and C2H2-enoLOGOS are accessible over the web at . PMID:15980495

A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group.

PubMed

Singh, Reema; Schilde, Christina; Schaap, Pauline

2016-11-17

Dictyostelia are a well-studied group of organisms with colonial multicellularity, which are members of the mostly unicellular Amoebozoa. A phylogeny based on SSU rDNA data subdivided all Dictyostelia into four major groups, but left the position of the root and of six group-intermediate taxa unresolved. Recent phylogenies inferred from 30 or 213 proteins from sequenced genomes, positioned the root between two branches, each containing two major groups, but lacked data to position the group-intermediate taxa. Since the positions of these early diverging taxa are crucial for understanding the evolution of phenotypic complexity in Dictyostelia, we sequenced six representative genomes of early diverging taxa. We retrieved orthologs of 47 housekeeping proteins with an average size of 890 amino acids from six newly sequenced and eight published genomes of Dictyostelia and unicellular Amoebozoa and inferred phylogenies from single and concatenated protein sequence alignments. Concatenated alignments of all 47 proteins, and four out of five subsets of nine concatenated proteins all produced the same consensus phylogeny with 100% statistical support. Trees inferred from just two out of the 47 proteins, individually reproduced the consensus phylogeny, highlighting that single gene phylogenies will rarely reflect correct species relationships. However, sets of two or three concatenated proteins again reproduced the consensus phylogeny, indicating that a small selection of genes suffices for low cost classification of as yet unincorporated or newly discovered dictyostelid and amoebozoan taxa by gene amplification. The multi-locus consensus phylogeny shows that groups 1 and 2 are sister clades in branch I, with the group-intermediate taxon D. polycarpum positioned as outgroup to group 2. Branch II consists of groups 3 and 4, with the group-intermediate taxon Polysphondylium violaceum positioned as sister to group 4, and the group-intermediate taxon Dictyostelium polycephalum branching at the base of that whole clade. Given the data, the approximately unbiased test rejects all alternative topologies favoured by SSU rDNA and individual proteins with high statistical support. The test also rejects monophyletic origins for the genera Acytostelium, Polysphondylium and Dictyostelium. The current position of Acytostelium ellipticum in the consensus phylogeny indicates that somatic cells were lost twice in Dictyostelia.

Transcription factor profiling reveals molecular choreography and key regulators of human retrotransposon expression

PubMed Central

Sun, Xiaoji; Wang, Xuya; Tang, Zuojian; Grivainis, Mark; Kahler, David; Yun, Chi; Mita, Paolo; Fenyö, David

2018-01-01

Transposable elements (TEs) represent a substantial fraction of many eukaryotic genomes, and transcriptional regulation of these factors is important to determine TE activities in human cells. However, due to the repetitive nature of TEs, identifying transcription factor (TF)-binding sites from ChIP-sequencing (ChIP-seq) datasets is challenging. Current algorithms are focused on subtle differences between TE copies and thus bias the analysis to relatively old and inactive TEs. Here we describe an approach termed “MapRRCon” (mapping repeat reads to a consensus) which allows us to identify proteins binding to TE DNA sequences by mapping ChIP-seq reads to the TE consensus sequence after whole-genome alignment. Although this method does not assign binding sites to individual insertions in the genome, it provides a landscape of interacting TFs by capturing factors that bind to TEs under various conditions. We applied this method to screen TFs’ interaction with L1 in human cells/tissues using ENCODE ChIP-seq datasets and identified 178 of the 512 TFs tested as bound to L1 in at least one biological condition with most of them (138) localized to the promoter. Among these L1-binding factors, we focused on Myc and CTCF, as they play important roles in cancer progression and 3D chromatin structure formation. Furthermore, we explored the transcriptomes of The Cancer Genome Atlas breast and ovarian tumor samples in which a consistent anti-/correlation between L1 and Myc/CTCF expression was observed, suggesting that these two factors may play roles in regulating L1 transcription during the development of such tumors. PMID:29802231

Harmonising data collection from osteoarthritis studies to enable stratification: recommendations on core data collection from an Arthritis Research UK clinical studies group.

PubMed

Kingsbury, Sarah R; Corp, Nadia; Watt, Fiona E; Felson, David T; O'Neill, Terence W; Holt, Cathy A; Jones, Richard K; Conaghan, Philip G; Arden, Nigel K

2016-08-01

Treatment of OA by stratifying for commonly used and novel therapies will likely improve the range of effective therapy options and their rational deployment in this undertreated, chronic disease. In order to develop appropriate datasets for conducting post hoc analyses to inform approaches to stratification for OA, our aim was to develop recommendations on the minimum data that should be recorded at baseline in all future OA interventional and observational studies. An Arthritis Research UK study group comprised of 32 experts used a Delphi-style approach supported by a literature review of systematic reviews to come to a consensus on core data collection for OA studies. Thirty-five systematic reviews were used as the basis for the consensus group discussion. For studies with a primary structural endpoint, core domains for collection were defined as BMI, age, gender, racial origin, comorbidities, baseline OA pain, pain in other joints and occupation. In addition to the items generalizable to all anatomical sites, joint-specific domains included radiographic measures, surgical history and anatomical factors, including alignment. To demonstrate clinical relevance for symptom studies, the collection of mental health score, self-efficacy and depression scales were advised in addition to the above. Currently it is not possible to stratify patients with OA into therapeutic groups. A list of core and optional data to be collected in all OA interventional and observational studies was developed, providing a basis for future analyses to identify predictors of progression or response to treatment. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Rheumatology.

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

PubMed Central

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

2016-01-01

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

Evaluating Test Validity: Reprise and Progress

ERIC Educational Resources Information Center

Shepard, Lorrie A.

2016-01-01

The AERA, APA, NCME Standards define validity as "the degree to which evidence and theory support the interpretations of test scores for proposed uses of tests". A century of disagreement about validity does not mean that there has not been substantial progress. This consensus definition brings together interpretations and use so that it…

Stereochemical analysis of the functional significance of the conserved inverted CCAAT and TATA elements in the rat bone sialoprotein gene promoter.

PubMed

Su, Ming; Lee, Daniel; Ganss, Bernhard; Sodek, Jaro

2006-04-14

Basal transcription of the bone sialoprotein gene is mediated by highly conserved inverted CCAAT (ICE; ATTGG) and TATA elements (TTTATA) separated by precisely 21 nucleotides. Here we studied the importance of the relative position and orientation of the CCAAT and TATA elements in the proximal promoter by measuring the transcriptional activity of a series of mutated reporter constructs in transient transfection assays. Whereas inverting the TTTATA (wild type) to a TATAAA (consensus TATA) sequence increased transcription slightly, transcription was reduced when the flanking dinucleotides were also inverted. In contrast, reversing the ATTGG (wild type; ICE) to a CCAAT (RICE) sequence caused a marked reduction in transcription, whereas both transcription and NF-Y binding were progressively increased with the simultaneous inversion of flanking nucleotides (f-RICE-f). Reducing the distance between the ICE and TATA elements produced cyclical changes in transcriptional activity that correlated with progressive alterations in the relative positions of the CCAAT and TATA elements on the face of the DNA helix. Minimal transcription was observed after 5 nucleotides were deleted (equivalent to approximately one half turn of the helix), whereas transcription was fully restored after deleting 10 nucleotides (approximately one full turn of the DNA helix), transcriptional activity being progressively lost with deletions beyond 10 nucleotides. In comparison, when deletions were made with the ICE in the reversed (f-RICE-f) orientation transcriptional activity was progressively lost with no recovery. These results show that, although transcription can still occur when the CCAAT box is reversed and/or displaced relative to the TATA box, the activity is dependent upon the flexibility of the intervening DNA helix needed to align the NF-Y complex on the CCAAT box with preinitiation complex proteins that bind to the TATA box. Thus, the precise location and orientation of the CCAAT element is necessary for optimizing basal transcription of the bone sialoprotein gene.

Paratonia: a Delphi procedure for consensus definition.

PubMed

Hobbelen, Johannes S M; Koopmans, Raymond T C M; Verhey, Frans R J; Van Peppen, Roland P S; de Bie, Rob A

2006-01-01

Paratonia is a motor problem that develops during the course of dementia. Definitions of paratonia used in the literature differ considerably, which has clinical implications and may lead to an undesirable heterogeneity in study populations. For this reason, we initiated a Delphi procedure with known experts in the field to establish an operational consensus definition of paratonia. The Delphi procedure involved an anonymous and multistage approach presented as a questionnaire, with each stage building on the results of the previous one in order to reach consensus on the definition of paratonia. Eight of 17 experts agreed to participate in the study. After 4 rounds, the participants reached consensus on the following definition: paratonia is a form of hypertonia with an involuntary variable resistance during passive movement. The nature of paratonia may change with progression of dementia (eg, from active assistance (aka Mitgehen) to active resistance). The degree of resistance depends on the speed of movement (eg, slow > low resistance, fast > high resistance). The degree of paratonia is proportional to the amount of force applied and increases with progression of dementia. The resistance to passive movement is in any direction and there is no clasp-knife phenomenon. The Delphi procedure resulted in a comprehensive, operational definition of paratonia. Future research should focus on the reliability and validity of this definition.

Identifying patients and clinical scenarios for use of long-acting injectable antipsychotics - expert consensus survey part 1.

PubMed

Sajatovic, Martha; Ross, Ruth; Legacy, Susan N; Correll, Christoph U; Kane, John M; DiBiasi, Faith; Fitzgerald, Heather; Byerly, Matthew

2018-01-01

To assess expert consensus on barriers and facilitators for long-acting injectable antipsychotic (LAI) use and provide clinical recommendations on issues where clinical evidence is lacking, including identifying appropriate clinical situations for LAI use. A 50-question survey comprising 916 response options was distributed to 42 research experts and high prescribers with extensive LAI experience. Respondents rated options on relative appropriateness/importance using a 9-point scale. Consensus was determined using chi-square test of score distributions. Mean (standard deviation) ratings were calculated. Responses to 29 questions (577 options) relating to appropriate patients and clinical scenarios for LAI use are reported. Recommendations aligned with research on risk factors for nonadherence and poor outcomes for patients with schizophrenia/schizoaffective or bipolar disorder. Findings suggested, contrary to general practice patterns, that LAI use may be appropriate earlier in the disease course and in younger patients. Results for bipolar disorder were similar to those for schizophrenia but with less consensus. Numerous facilitators of LAI prescribing were considered important, particularly that LAIs may reduce relapses and improve outcomes. Findings support wider use of LAIs in patients with schizophrenia/schizoaffective and bipolar disorders beyond the setting of poor adherence and earlier use in the disease course.

rVISTA 2.0: Evolutionary Analysis of Transcription Factor Binding Sites

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

Loots, G G; Ovcharenko, I

2004-01-28

Identifying and characterizing the patterns of DNA cis-regulatory modules represents a challenge that has the potential to reveal the regulatory language the genome uses to dictate transcriptional dynamics. Several studies have demonstrated that regulatory modules are under positive selection and therefore are often conserved between related species. Using this evolutionary principle we have created a comparative tool, rVISTA, for analyzing the regulatory potential of noncoding sequences. The rVISTA tool combines transcription factor binding site (TFBS) predictions, sequence comparisons and cluster analysis to identify noncoding DNA regions that are highly conserved and present in a specific configuration within an alignment. Heremore » we present the newly developed version 2.0 of the rVISTA tool that can process alignments generated by both zPicture and PipMaker alignment programs or use pre-computed pairwise alignments of seven vertebrate genomes available from the ECR Browser. The rVISTA web server is closely interconnected with the TRANSFAC database, allowing users to either search for matrices present in the TRANSFAC library collection or search for user-defined consensus sequences. rVISTA tool is publicly available at http://rvista.dcode.org/.« less

Progressive Modularization: Reframing Our Understanding of Typical and Atypical Language Development

ERIC Educational Resources Information Center

D'Souza, Dean; Filippi, Roberto

2017-01-01

The ability to acquire language is a critical part of human development. Yet there is no consensus on how the skill emerges in early development. Does it constitute an innately-specified, language-processing module or is it acquired progressively? One of Annette Karmiloff-Smith's (1938-2016) key contributions to developmental science addresses…

Draft Genome Sequences of Two Novel Salmonella enterica subsp. enterica Strains Isolated from Low-Moisture Foods with Applications in Food Safety Research.

PubMed

Radford, Devon R; Leon-Velarde, Carlos G; Chen, Shu; Hamidi Oskouei, Amir M; Balamurugan, Sampathkumar

2018-03-29

The genomes of two strains of Salmonella enterica subsp. enterica serovar Cubana and serovar Muenchen, isolated from dry hazelnuts and chia seeds, respectively, were sequenced using the Illumina MiSeq platform, assembled de novo using the overlap-layout-consensus method, and aligned to their respective most identical sequence genome scaffolds using MUMMER and BLAST searches. Copyright © 2018 Radford et al.

Biclustering as a method for RNA local multiple sequence alignment.

PubMed

Wang, Shu; Gutell, Robin R; Miranker, Daniel P

2007-12-15

Biclustering is a clustering method that simultaneously clusters both the domain and range of a relation. A challenge in multiple sequence alignment (MSA) is that the alignment of sequences is often intended to reveal groups of conserved functional subsequences. Simultaneously, the grouping of the sequences can impact the alignment; precisely the kind of dual situation biclustering is intended to address. We define a representation of the MSA problem enabling the application of biclustering algorithms. We develop a computer program for local MSA, BlockMSA, that combines biclustering with divide-and-conquer. BlockMSA simultaneously finds groups of similar sequences and locally aligns subsequences within them. Further alignment is accomplished by dividing both the set of sequences and their contents. The net result is both a multiple sequence alignment and a hierarchical clustering of the sequences. BlockMSA was tested on the subsets of the BRAliBase 2.1 benchmark suite that display high variability and on an extension to that suite to larger problem sizes. Also, alignments were evaluated of two large datasets of current biological interest, T box sequences and Group IC1 Introns. The results were compared with alignments computed by ClustalW, MAFFT, MUCLE and PROBCONS alignment programs using Sum of Pairs (SPS) and Consensus Count. Results for the benchmark suite are sensitive to problem size. On problems of 15 or greater sequences, BlockMSA is consistently the best. On none of the problems in the test suite are there appreciable differences in scores among BlockMSA, MAFFT and PROBCONS. On the T box sequences, BlockMSA does the most faithful job of reproducing known annotations. MAFFT and PROBCONS do not. On the Intron sequences, BlockMSA, MAFFT and MUSCLE are comparable at identifying conserved regions. BlockMSA is implemented in Java. Source code and supplementary datasets are available at http://aug.csres.utexas.edu/msa/

Polyethylene damage and deformation on fixed-bearing, non-conforming unicondylar knee replacements corresponding to progressive changes in alignment and fixation.

PubMed

Harman, Melinda K; Schmitt, Sabine; Rössing, Sven; Banks, Scott A; Sharf, Hans-Peter; Viceconti, Marco; Hodge, W Andrew

2010-07-01

Deviations from nominal alignment of unicondylar knee replacements impact knee biomechanics, including the load and stress distribution at the articular contact surfaces. This study characterizes relationships between the biomechanical environment, distinguished by progressive changes in alignment and fixation, and articular damage and deformation in a consecutive series of retrieved unicondylar knee replacements. Twenty seven fixed-bearing, non-conforming unicondylar knee replacements of one design were retrieved after 2 to 13 years of in vivo function. The in vivo biomechanical environment was characterized by grading component migration measured from full-length radiographs and grading component fixation based on intraoperative manual palpation. Articular damage patterns and linear deformation on the polyethylene inserts were measured using optical photogrammetry and contact point digitization. Articular damage patterns and surface deformation on the explanted polyethylene inserts corresponded to progressive changes in component alignment and fixation. Component migration produced higher deformation rates, whereas loosening contributed to larger damage areas but lower deformation rates. Migration and loosening of the femoral component, but not the tibial component, were factors contributing to large regions of abrasion concentrated on the articular periphery. Classifying component migration and fixation at revision proved useful for distinguishing common biomechanical conditions associated with the varied polyethylene damage patterns and linear deformation for this fixed-bearing, non-conforming design. Pre-clinical evaluations of unicondylar knee replacements that are capable of reproducing variations in clinical alignment and predicting the observed wear mechanisms are necessary to better understand the impact of knee biomechanics and design on unicondylar knee replacement longevity. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

[The Chinese experts' consensus on the evaluation and management of asthma exacerbation].

PubMed

2018-01-01

Asthma exacerbations can do a lot of harm to the patients and consume large amounts of medical resources. This consensus is based on the domestic and foreign guidelines and literatures to standardize the evaluation and management of asthma exacerbations in China. Asthma exacerbations are characterized by a progressive increase in symptoms of shortness of breath, cough, wheezing or chest tightness and progressive decrease in lung function, and usually require modification of treatment. Recognizing risk factors and triggering factors of asthma exacerbations is helpful for the prevention and long-term management. Evaluation of asthma exacerbations is based on symptoms, lung function, and arterial blood gas. Management is stratified according to the severity of disease. Different regimens to treat asthma exacerbations are discussed in this consensus. Glucocorticoids should be used properly. Overuse of antibiotics should be avoided. Management of life-threatening asthma is discussed separately. Special attention should be paid in some special respects, such as asthma during peri-operation period, gestation period, and childhood. Diagnosis and management of complications are also of great significance and are discussed in details.

Tracing the Assessment Triangle with Learning Progression-Aligned Assessments in Mathematics

ERIC Educational Resources Information Center

Lai, Emily R.; Kobrin, Jennifer L.; DiCerbo, Kristen E.; Holland, Laura R.

2017-01-01

We describe an application of the assessment triangle, using a learning progression as the "cognition" vertex. We summarize two studies to evaluate whether evidence of student performance is consistent with our progression. In Study 1, we conducted think alouds using draft assessment activities and evaluated responses in relation to the…

The Role of Language Learning Progressions in Improved Instruction and Assessment of English Language Learners

ERIC Educational Resources Information Center

Bailey, Alison L.; Heritage, Margaret

2014-01-01

This article addresses theoretical and empirical issues relevant for the development and evaluation of language learning progressions. The authors explore how learning progressions aligned with new content standards can form a central basis of efforts to describe the English language needed in school contexts for learning, instruction, and…

Nursing physical assessment for patient safety in general wards: reaching consensus on core skills.

PubMed

Douglas, Clint; Booker, Catriona; Fox, Robyn; Windsor, Carol; Osborne, Sonya; Gardner, Glenn

2016-07-01

To determine consensus across acute care specialty areas on core physical assessment skills necessary for early recognition of changes in patient status in general wards. Current approaches to physical assessment are inconsistent and have not evolved to meet increased patient and system demands. New models of nursing assessment are needed in general wards that ensure a proactive and patient safety approach. A modified Delphi study. Focus group interviews with 150 acute care registered nurses at a large tertiary referral hospital generated a framework of core skills that were developed into a web-based survey. We then sought consensus with a panel of 35 senior acute care registered nurses following a classical Delphi approach over three rounds. Consensus was predefined as at least 80% agreement for each skill across specialty areas. Content analysis of focus group transcripts identified 40 discrete core physical assessment skills. In the Delphi rounds, 16 of these were consensus validated as core skills and were conceptually aligned with the primary survey: (Airway) Assess airway patency; (Breathing) Measure respiratory rate, Evaluate work of breathing, Measure oxygen saturation; (Circulation) Palpate pulse rate and rhythm, Measure blood pressure by auscultation, Assess urine output; (Disability) Assess level of consciousness, Evaluate speech, Assess for pain; (Exposure) Measure body temperature, Inspect skin integrity, Inspect and palpate skin for signs of pressure injury, Observe any wounds, dressings, drains and invasive lines, Observe ability to transfer and mobilise, Assess bowel movements. Among a large and diverse group of experienced acute care registered nurses consensus was achieved on a structured core physical assessment to detect early changes in patient status. Although further research is needed to refine the model, clinical application should promote systematic assessment and clinical reasoning at the bedside. © 2016 John Wiley & Sons Ltd.

Updating OSHA Standards Based on National Consensus Standards; Eye and Face Protection. Final rule.

PubMed

2016-03-25

On March 13, 2015, OSHA published in the Federal Register a notice of proposed rulemaking (NPRM) to revise its eye and face protection standards for general industry, shipyard employment, marine terminals, longshoring, and construction by updating the references to national consensus standards approved by the American National Standards Institute (ANSI). OSHA received no significant objections from commenters and therefore is adopting the amendments as proposed. This final rule updates the references in OSHA's eye and face standards to reflect the most recent edition of the ANSI/International Safety Equipment Association (ISEA) eye and face protection standard. It removes the oldest-referenced edition of the same ANSI standard. It also amends other provisions of the construction eye and face protection standard to bring them into alignment with OSHA's general industry and maritime standards.

An Official American Thoracic Society Statement: Update on the Mechanisms, Assessment, and Management of Dyspnea

PubMed Central

Parshall, Mark B.; Schwartzstein, Richard M.; Adams, Lewis; Banzett, Robert B.; Manning, Harold L.; Bourbeau, Jean; Calverley, Peter M.; Gift, Audrey G.; Harver, Andrew; Lareau, Suzanne C.; Mahler, Donald A.; Meek, Paula M.; O'Donnell, Denis E.

2012-01-01

Background: Dyspnea is a common, distressing symptom of cardiopulmonary and neuromuscular diseases. Since the ATS published a consensus statement on dyspnea in 1999, there has been enormous growth in knowledge about the neurophysiology of dyspnea and increasing interest in dyspnea as a patient-reported outcome. Purpose: The purpose of this document is to update the 1999 ATS Consensus Statement on dyspnea. Methods: An interdisciplinary committee of experts representing ATS assemblies on Nursing, Clinical Problems, Sleep and Respiratory Neurobiology, Pulmonary Rehabilitation, and Behavioral Science determined the overall scope of this update through group consensus. Focused literature reviews in key topic areas were conducted by committee members with relevant expertise. The final content of this statement was agreed upon by all members. Results: Progress has been made in clarifying mechanisms underlying several qualitatively and mechanistically distinct breathing sensations. Brain imaging studies have consistently shown dyspnea stimuli to be correlated with activation of cortico-limbic areas involved with interoception and nociception. Endogenous and exogenous opioids may modulate perception of dyspnea. Instruments for measuring dyspnea are often poorly characterized; a framework is proposed for more consistent identification of measurement domains. Conclusions: Progress in treatment of dyspnea has not matched progress in elucidating underlying mechanisms. There is a critical need for interdisciplinary translational research to connect dyspnea mechanisms with clinical treatment and to validate dyspnea measures as patient-reported outcomes for clinical trials. PMID:22336677

Beyond Subprime Learning: Accelerating Progress in Early Education. Policy Brief

ERIC Educational Resources Information Center

Bornfreund, Laura; McCann, Clare; Williams, Conor; Guernsey, Lisa

2014-01-01

Earlier this year, in "Subprime Learning: Early Education in America since the Great Recession," the current state of early education in the U.S. was surveyed by examining progress over the last five years . It was found that while the public, political, and research consensus is stronger than ever, the field remains in dire need of…

Development of a group work assessment pedagogy using constructive alignment theory.

PubMed

Croy, Suzanne R

2018-02-01

The purpose of this paper is to explore group work assessment underpinned by constructive alignment theory to develop a new assessment pedagogy. A review was undertaken of an existing module 'Mental Health Nursing 1', with student nurses participating in the BSc (Hons) Nursing Programme. Constructive alignment theory requires teachers to adopt a deep approach to learning where module learning outcomes are aligned with the teaching environment and modes of assessment. As the module progressed, reviewing the Mental Health Nursing 1 module became an excellent opportunity to begin to understand how constructive alignment theory can inform a group work assessment pedagogy. Working using a constructively aligned assessment process became a valuable learning experience for the module leader whilst at the same time revealed a gap in the research around the impact of constructively aligned teaching and group work assessment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Simple chained guide trees give high-quality protein multiple sequence alignments

PubMed Central

Boyce, Kieran; Sievers, Fabian; Higgins, Desmond G.

2014-01-01

Guide trees are used to decide the order of sequence alignment in the progressive multiple sequence alignment heuristic. These guide trees are often the limiting factor in making large alignments, and considerable effort has been expended over the years in making these quickly or accurately. In this article we show that, at least for protein families with large numbers of sequences that can be benchmarked with known structures, simple chained guide trees give the most accurate alignments. These also happen to be the fastest and simplest guide trees to construct, computationally. Such guide trees have a striking effect on the accuracy of alignments produced by some of the most widely used alignment packages. There is a marked increase in accuracy and a marked decrease in computational time, once the number of sequences goes much above a few hundred. This is true, even if the order of sequences in the guide tree is random. PMID:25002495

Consensus-based training and assessment model for general surgery.

PubMed

Szasz, P; Louridas, M; de Montbrun, S; Harris, K A; Grantcharov, T P

2016-05-01

Surgical education is becoming competency-based with the implementation of in-training milestones. Training guidelines should reflect these changes and determine the specific procedures for such milestone assessments. This study aimed to develop a consensus view regarding operative procedures and tasks considered appropriate for junior and senior trainees, and the procedures that can be used as technical milestone assessments for trainee progression in general surgery. A Delphi process was followed where questionnaires were distributed to all 17 Canadian general surgery programme directors. Items were ranked on a 5-point Likert scale, with consensus defined as Cronbach's α of at least 0·70. Items rated 4 or above on the 5-point Likert scale by 80 per cent of the programme directors were included in the models. Two Delphi rounds were completed, with 14 programme directors taking part in round one and 11 in round two. The overall consensus was high (Cronbach's α = 0·98). The training model included 101 unique procedures and tasks, 24 specific to junior trainees, 68 specific to senior trainees, and nine appropriate to all. The assessment model included four procedures. A system of operative procedures and tasks for junior- and senior-level trainees has been developed along with an assessment model for trainee progression. These can be used as milestones in competency-based assessments. © 2016 BJS Society Ltd Published by John Wiley & Sons Ltd.

Is It Working? Distractor Analysis Results from the Test Of Astronomy STandards (TOAST) Assessment Instrument

NASA Astrophysics Data System (ADS)

Slater, Stephanie

2009-05-01

The Test Of Astronomy STandards (TOAST) assessment instrument is a multiple-choice survey tightly aligned to the consensus learning goals stated by the American Astronomical Society - Chair's Conference on ASTRO 101, the American Association of the Advancement of Science's Project 2061 Benchmarks, and the National Research Council's National Science Education Standards. Researchers from the Cognition in Astronomy, Physics and Earth sciences Research (CAPER) Team at the University of Wyoming's Science and Math Teaching Center (UWYO SMTC) have been conducting a question-by-question distractor analysis procedure to determine the sensitivity and effectiveness of each item. In brief, the frequency each possible answer choice, known as a foil or distractor on a multiple-choice test, is determined and compared to the existing literature on the teaching and learning of astronomy. In addition to having statistical difficulty and discrimination values, a well functioning assessment item will show students selecting distractors in the relative proportions to how we expect them to respond based on known misconceptions and reasoning difficulties. In all cases, our distractor analysis suggests that all items are functioning as expected. These results add weight to the validity of the Test Of Astronomy STandards (TOAST) assessment instrument, which is designed to help instructors and researchers measure the impact of course-length duration instructional strategies for undergraduate science survey courses with learning goals tightly aligned to the consensus goals of the astronomy education community.

SeqMule: automated pipeline for analysis of human exome/genome sequencing data.

PubMed

Guo, Yunfei; Ding, Xiaolei; Shen, Yufeng; Lyon, Gholson J; Wang, Kai

2015-09-18

Next-generation sequencing (NGS) technology has greatly helped us identify disease-contributory variants for Mendelian diseases. However, users are often faced with issues such as software compatibility, complicated configuration, and no access to high-performance computing facility. Discrepancies exist among aligners and variant callers. We developed a computational pipeline, SeqMule, to perform automated variant calling from NGS data on human genomes and exomes. SeqMule integrates computational-cluster-free parallelization capability built on top of the variant callers, and facilitates normalization/intersection of variant calls to generate consensus set with high confidence. SeqMule integrates 5 alignment tools, 5 variant calling algorithms and accepts various combinations all by one-line command, therefore allowing highly flexible yet fully automated variant calling. In a modern machine (2 Intel Xeon X5650 CPUs, 48 GB memory), when fast turn-around is needed, SeqMule generates annotated VCF files in a day from a 30X whole-genome sequencing data set; when more accurate calling is needed, SeqMule generates consensus call set that improves over single callers, as measured by both Mendelian error rate and consistency. SeqMule supports Sun Grid Engine for parallel processing, offers turn-key solution for deployment on Amazon Web Services, allows quality check, Mendelian error check, consistency evaluation, HTML-based reports. SeqMule is available at http://seqmule.openbioinformatics.org.

A High-Density Consensus Map of Common Wheat Integrating Four Mapping Populations Scanned by the 90K SNP Array

PubMed Central

Wen, Weie; He, Zhonghu; Gao, Fengmei; Liu, Jindong; Jin, Hui; Zhai, Shengnan; Qu, Yanying; Xia, Xianchun

2017-01-01

A high-density consensus map is a powerful tool for gene mapping, cloning and molecular marker-assisted selection in wheat breeding. The objective of this study was to construct a high-density, single nucleotide polymorphism (SNP)-based consensus map of common wheat (Triticum aestivum L.) by integrating genetic maps from four recombinant inbred line populations. The populations were each genotyped using the wheat 90K Infinium iSelect SNP assay. A total of 29,692 SNP markers were mapped on 21 linkage groups corresponding to 21 hexaploid wheat chromosomes, covering 2,906.86 cM, with an overall marker density of 10.21 markers/cM. Compared with the previous maps based on the wheat 90K SNP chip detected 22,736 (76.6%) of the SNPs with consistent chromosomal locations, whereas 1,974 (6.7%) showed different chromosomal locations, and 4,982 (16.8%) were newly mapped. Alignment of the present consensus map and the wheat expressed sequence tags (ESTs) Chromosome Bin Map enabled assignment of 1,221 SNP markers to specific chromosome bins and 819 ESTs were integrated into the consensus map. The marker orders of the consensus map were validated based on physical positions on the wheat genome with Spearman rank correlation coefficients ranging from 0.69 (4D) to 0.97 (1A, 4B, 5B, and 6A), and were also confirmed by comparison with genetic position on the previously 40K SNP consensus map with Spearman rank correlation coefficients ranging from 0.84 (6D) to 0.99 (6A). Chromosomal rearrangements reported previously were confirmed in the present consensus map and new putative rearrangements were identified. In addition, an integrated consensus map was developed through the combination of five published maps with ours, containing 52,607 molecular markers. The consensus map described here provided a high-density SNP marker map and a reliable order of SNPs, representing a step forward in mapping and validation of chromosomal locations of SNPs on the wheat 90K array. Moreover, it can be used as a reference for quantitative trait loci (QTL) mapping to facilitate exploitation of genes and QTL in wheat breeding. PMID:28848588

AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences

PubMed Central

2010-01-01

Background Multiple sequence alignments are used to study gene or protein function, phylogenetic relations, genome evolution hypotheses and even gene polymorphisms. Virtually without exception, all available tools focus on conserved segments or residues. Small divergent regions, however, are biologically important for specific quantitative polymerase chain reaction, genotyping, molecular markers and preparation of specific antibodies, and yet have received little attention. As a consequence, they must be selected empirically by the researcher. AlignMiner has been developed to fill this gap in bioinformatic analyses. Results AlignMiner is a Web-based application for detection of conserved and divergent regions in alignments of conserved sequences, focusing particularly on divergence. It accepts alignments (protein or nucleic acid) obtained using any of a variety of algorithms, which does not appear to have a significant impact on the final results. AlignMiner uses different scoring methods for assessing conserved/divergent regions, Entropy being the method that provides the highest number of regions with the greatest length, and Weighted being the most restrictive. Conserved/divergent regions can be generated either with respect to the consensus sequence or to one master sequence. The resulting data are presented in a graphical interface developed in AJAX, which provides remarkable user interaction capabilities. Users do not need to wait until execution is complete and can.even inspect their results on a different computer. Data can be downloaded onto a user disk, in standard formats. In silico and experimental proof-of-concept cases have shown that AlignMiner can be successfully used to designing specific polymerase chain reaction primers as well as potential epitopes for antibodies. Primer design is assisted by a module that deploys several oligonucleotide parameters for designing primers "on the fly". Conclusions AlignMiner can be used to reliably detect divergent regions via several scoring methods that provide different levels of selectivity. Its predictions have been verified by experimental means. Hence, it is expected that its usage will save researchers' time and ensure an objective selection of the best-possible divergent region when closely related sequences are analysed. AlignMiner is freely available at http://www.scbi.uma.es/alignminer. PMID:20525162

Highlighting clinical needs in Clostridium difficile infection: the views of European healthcare professionals at the front line.

PubMed

Aguado, J M; Anttila, V J; Galperine, T; Goldenberg, S D; Gwynn, S; Jenkins, D; Norén, T; Petrosillo, N; Seifert, H; Stallmach, A; Warren, T; Wenisch, C

2015-06-01

Clostridium difficile infection (CDI) is the leading cause of infectious nosocomial diarrhoea in Europe. Despite increased focus, its incidence and severity are increasing in many European countries. We developed a series of consensus statements to identify unmet clinical needs in the recognition and management of CDI. A consortium of European experts prepared a series of 29 statements representing their collective views on the diagnosis and management of CDI in Europe. The statements were grouped into the following six broad themes: diagnosis; definitions of severity; treatment failure, recurrence and its consequences; infection prevention and control interventions; education and antimicrobial stewardship; and National CDI clinical guidance and policy. These statements were reviewed using questionnaires by 1047 clinicians involved in managing CDI, who indicated their level of agreement with each statement. Levels of agreement exceeded the 66% threshold for consensus for 27 out of 29 statements (93.1%), indicating strong support. Variance between countries and specialties was analysed and showed strong alignment with the overall consensus scores. Based on the consensus scores of the respondent group, recommendations are suggested for the further development of CDI services in order to reduce transmission and recurrence and to ensure that appropriate diagnosis and treatment strategies are applied across all healthcare settings. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Protein contact prediction by integrating deep multiple sequence alignments, coevolution and machine learning.

PubMed

Adhikari, Badri; Hou, Jie; Cheng, Jianlin

2018-03-01

In this study, we report the evaluation of the residue-residue contacts predicted by our three different methods in the CASP12 experiment, focusing on studying the impact of multiple sequence alignment, residue coevolution, and machine learning on contact prediction. The first method (MULTICOM-NOVEL) uses only traditional features (sequence profile, secondary structure, and solvent accessibility) with deep learning to predict contacts and serves as a baseline. The second method (MULTICOM-CONSTRUCT) uses our new alignment algorithm to generate deep multiple sequence alignment to derive coevolution-based features, which are integrated by a neural network method to predict contacts. The third method (MULTICOM-CLUSTER) is a consensus combination of the predictions of the first two methods. We evaluated our methods on 94 CASP12 domains. On a subset of 38 free-modeling domains, our methods achieved an average precision of up to 41.7% for top L/5 long-range contact predictions. The comparison of the three methods shows that the quality and effective depth of multiple sequence alignments, coevolution-based features, and machine learning integration of coevolution-based features and traditional features drive the quality of predicted protein contacts. On the full CASP12 dataset, the coevolution-based features alone can improve the average precision from 28.4% to 41.6%, and the machine learning integration of all the features further raises the precision to 56.3%, when top L/5 predicted long-range contacts are evaluated. And the correlation between the precision of contact prediction and the logarithm of the number of effective sequences in alignments is 0.66. © 2017 Wiley Periodicals, Inc.

The protein structure prediction problem could be solved using the current PDB library

PubMed Central

Zhang, Yang; Skolnick, Jeffrey

2005-01-01

For single-domain proteins, we examine the completeness of the structures in the current Protein Data Bank (PDB) library for use in full-length model construction of unknown sequences. To address this issue, we employ a comprehensive benchmark set of 1,489 medium-size proteins that cover the PDB at the level of 35% sequence identity and identify templates by structure alignment. With homologous proteins excluded, we can always find similar folds to native with an average rms deviation (RMSD) from native of 2.5 Å with ≈82% alignment coverage. These template structures often contain a significant number of insertions/deletions. The tasser algorithm was applied to build full-length models, where continuous fragments are excised from the top-scoring templates and reassembled under the guide of an optimized force field, which includes consensus restraints taken from the templates and knowledge-based statistical potentials. For almost all targets (except for 2/1,489), the resultant full-length models have an RMSD to native below 6 Å (97% of them below 4 Å). On average, the RMSD of full-length models is 2.25 Å, with aligned regions improved from 2.5 Å to 1.88 Å, comparable with the accuracy of low-resolution experimental structures. Furthermore, starting from state-of-the-art structural alignments, we demonstrate a methodology that can consistently bring template-based alignments closer to native. These results are highly suggestive that the protein-folding problem can in principle be solved based on the current PDB library by developing efficient fold recognition algorithms that can recover such initial alignments. PMID:15653774

A short note on dynamic programming in a band.

PubMed

Gibrat, Jean-François

2018-06-15

Third generation sequencing technologies generate long reads that exhibit high error rates, in particular for insertions and deletions which are usually the most difficult errors to cope with. The only exact algorithm capable of aligning sequences with insertions and deletions is a dynamic programming algorithm. In this note, for the sake of efficiency, we consider dynamic programming in a band. We show how to choose the band width in function of the long reads' error rates, thus obtaining an [Formula: see text] algorithm in space and time. We also propose a procedure to decide whether this algorithm, when applied to semi-global alignments, provides the optimal score. We suggest that dynamic programming in a band is well suited to the problem of aligning long reads between themselves and can be used as a core component of methods for obtaining a consensus sequence from the long reads alone. The function implementing the dynamic programming algorithm in a band is available, as a standalone program, at: https://forgemia.inra.fr/jean-francois.gibrat/BAND_DYN_PROG.git.

WebLogo: A Sequence Logo Generator

PubMed Central

Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc; Brenner, Steven E.

2004-01-01

WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment. Sequence logos provide a richer and more precise description of sequence similarity than consensus sequences and can rapidly reveal significant features of the alignment otherwise difficult to perceive. Each logo consists of stacks of letters, one stack for each position in the sequence. The overall height of each stack indicates the sequence conservation at that position (measured in bits), whereas the height of symbols within the stack reflects the relative frequency of the corresponding amino or nucleic acid at that position. WebLogo has been enhanced recently with additional features and options, to provide a convenient and highly configurable sequence logo generator. A command line interface and the complete, open WebLogo source code are available for local installation and customization. PMID:15173120

Diagnosis and Management of Iliac Artery Endofibrosis: Results of a Delphi Consensus Study.

PubMed

2016-07-01

Iliac endofibrosis is a rare condition that may result in a reduction of blood flow to the lower extremity in young, otherwise healthy individuals. The data to inform everyday clinical management are weak and therefore a Delphi consensus methodology was used to explore areas of consensus and disagreement concerning the diagnosis and management of patients with suspected iliac endofibrosis. A three-round Delphi questionnaire approach was used among vascular surgeons, sports physicians, sports scientists, radiologists, and clinical vascular scientists with experience of treating this condition to explore diagnosis and clinical management issues for patients with suspected iliac artery endofibrosis. Analysis is based on 18 responses to round 2 and 14 responses to round 3, with agreement reported when 70% of respondents were in agreement. Initially there was agreement on the typical symptoms at presentation and the need for an exercise test in the diagnosis. Round 3 clarified that duplex ultrasound was a useful tool in the diagnosis of endofibrosis. There was consensus on the most appropriate type of surgery (endarterectomy and vein patch) and that endovascular interventions were inadvisable. The final round helped to inform aspects of the natural history and post-operative surveillance. Progression of the disease was likely with continued exercise but cessation may prevent progression. Surveillance after surgery is generally recommended yearly with at least a clinical assessment. There is broad agreement about the presenting symptoms and the investigations required to confirm (or exclude) the diagnosis of iliac endofibrosis. There was consensus on the surgical approach to repair. Disagreement existed about the specific diagnostic criteria that should be applied during non-invasive testing and about post-operative care and resumption of exercise. Copyright © 2016 European Society for Vascular Surgery. Published by Elsevier Ltd. All rights reserved.

A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments.

PubMed

Robinson, Mark D; De Souza, David P; Keen, Woon Wai; Saunders, Eleanor C; McConville, Malcolm J; Speed, Terence P; Likić, Vladimir A

2007-10-29

Gas chromatography-mass spectrometry (GC-MS) is a robust platform for the profiling of certain classes of small molecules in biological samples. When multiple samples are profiled, including replicates of the same sample and/or different sample states, one needs to account for retention time drifts between experiments. This can be achieved either by the alignment of chromatographic profiles prior to peak detection, or by matching signal peaks after they have been extracted from chromatogram data matrices. Automated retention time correction is particularly important in non-targeted profiling studies. A new approach for matching signal peaks based on dynamic programming is presented. The proposed approach relies on both peak retention times and mass spectra. The alignment of more than two peak lists involves three steps: (1) all possible pairs of peak lists are aligned, and similarity of each pair of peak lists is estimated; (2) the guide tree is built based on the similarity between the peak lists; (3) peak lists are progressively aligned starting with the two most similar peak lists, following the guide tree until all peak lists are exhausted. When two or more experiments are performed on different sample states and each consisting of multiple replicates, peak lists within each set of replicate experiments are aligned first (within-state alignment), and subsequently the resulting alignments are aligned themselves (between-state alignment). When more than two sets of replicate experiments are present, the between-state alignment also employs the guide tree. We demonstrate the usefulness of this approach on GC-MS metabolic profiling experiments acquired on wild-type and mutant Leishmania mexicana parasites. We propose a progressive method to match signal peaks across multiple GC-MS experiments based on dynamic programming. A sensitive peak similarity function is proposed to balance peak retention time and peak mass spectra similarities. This approach can produce the optimal alignment between an arbitrary number of peak lists, and models explicitly within-state and between-state peak alignment. The accuracy of the proposed method was close to the accuracy of manually-curated peak matching, which required tens of man-hours for the analyzed data sets. The proposed approach may offer significant advantages for processing of high-throughput metabolomics data, especially when large numbers of experimental replicates and multiple sample states are analyzed.

Classification systems for causes of stillbirth and neonatal death, 2009-2014: an assessment of alignment with characteristics for an effective global system.

PubMed

Leisher, Susannah Hopkins; Teoh, Zheyi; Reinebrant, Hanna; Allanson, Emma; Blencowe, Hannah; Erwich, Jan Jaap; Frøen, J Frederik; Gardosi, Jason; Gordijn, Sanne; Gülmezoglu, A Metin; Heazell, Alexander E P; Korteweg, Fleurisca; Lawn, Joy; McClure, Elizabeth M; Pattinson, Robert; Smith, Gordon C S; Tunçalp, Ӧzge; Wojcieszek, Aleena M; Flenady, Vicki

2016-09-15

To reduce the burden of 5.3 million stillbirths and neonatal deaths annually, an understanding of causes of deaths is critical. A systematic review identified 81 systems for classification of causes of stillbirth (SB) and neonatal death (NND) between 2009 and 2014. The large number of systems hampers efforts to understand and prevent these deaths. This study aimed to assess the alignment of current classification systems with expert-identified characteristics for a globally effective classification system. Eighty-one classification systems were assessed for alignment with 17 characteristics previously identified through expert consensus as necessary for an effective global system. Data were extracted independently by two authors. Systems were assessed against each characteristic and weighted and unweighted scores assigned to each. Subgroup analyses were undertaken by system use, setting, type of death included and type of characteristic. None of the 81 systems were aligned with more than 9 of the 17 characteristics; most (82 %) were aligned with four or fewer. On average, systems were aligned with 19 % of characteristics. The most aligned system (Frøen 2009-Codac) still had an unweighted score of only 9/17. Alignment with individual characteristics ranged from 0 to 49 %. Alignment was somewhat higher for widely used as compared to less used systems (22 % v 17 %), systems used only in high income countries as compared to only in low and middle income countries (20 % vs 16 %), and systems including both SB and NND (23 %) as compared to NND-only (15 %) and SB-only systems (13 %). Alignment was higher with characteristics assessing structure (23 %) than function (15 %). There is an unmet need for a system exhibiting all the characteristics of a globally effective system as defined by experts in the use of systems, as none of the 81 contemporary classification systems assessed was highly aligned with these characteristics. A particular concern in terms of global effectiveness is the lack of alignment with "ease of use" among all systems, including even the most-aligned. A system which meets the needs of users would have the potential to become the first truly globally effective classification system.

Axelrod model: accepting or discussing

NASA Astrophysics Data System (ADS)

Dybiec, Bartlomiej; Mitarai, Namiko; Sneppen, Kim

2012-10-01

Agents building social systems are characterized by complex states, and interactions among individuals can align their opinions. The Axelrod model describes how local interactions can result in emergence of cultural domains. We propose two variants of the Axelrod model where local consensus is reached either by listening and accepting one of neighbors' opinion or two agents discuss their opinion and achieve an agreement with mixed opinions. We show that the local agreement rule affects the character of the transition between the single culture and the multiculture regimes.

Progress in ETA-II magnetic field alignment using stretched wire and low energy electron beam techniques

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

Deadrick, F.J.; Griffith, L.V.

1990-08-17

Flux line alignment of the solenoidal focus magnets used on the ETA-II linear induction accelerator is a key element leading to a reduction of beam corkscrew motion. Two techniques have been used on the ETA-II accelerator to measure and establish magnet alignment. A low energy electron beam has been used to directly map magnetic field lines, and recent work has utilized a pulsed stretched wire technique to measure magnet tilts and offsets with respect to a reference axis. This paper reports on the techniques used in the ETA-II accelerator alignment, and presents results from those measurements which show that acceleratormore » is magnetically aligned to within {approximately}{plus minus}200 microns. 3 refs., 8 figs.« less

Genetic map of artichoke × wild cardoon: toward a consensus map for Cynara cardunculus.

PubMed

Sonnante, Gabriella; Gatto, Angela; Morgese, Anita; Montemurro, Francesco; Sarli, Giulio; Blanco, Emanuela; Pignone, Domenico

2011-11-01

An integrated consensus linkage map is proposed for globe artichoke. Maternal and paternal genetic maps were constructed on the basis of an F(1) progeny derived from crossing an artichoke genotype (Mola) with its progenitor, the wild cardoon (Tolfa), using EST-derived SSRs, genomic SSRs, AFLPs, ten genes, and two morphological traits. For most genes, mainly belonging to the chlorogenic acid pathway, new markers were developed. Five of these were SNP markers analyzed through high-resolution melt technology. From the maternal (Mola) and paternal (Tolfa) maps, an integrated map was obtained, containing 337 molecular and one morphological markers ordered in 17 linkage groups (LGs), linked between Mola and Tolfa. The integrated map covers 1,488.8 cM, with an average distance of 4.4 cM between markers. The map was aligned with already existing maps for artichoke, and 12 LGs were linked via 31 bridge markers. LG numbering has been proposed. A total of 124 EST-SSRs and two genes were mapped here for the first time, providing a framework for the construction of a functional map in artichoke. The establishment of a consensus map represents a necessary condition to plan a complete sequencing of the globe artichoke genome.

Predicting the transmembrane secondary structure of ligand-gated ion channels.

PubMed

Bertaccini, E; Trudell, J R

2002-06-01

Recent mutational analyses of ligand-gated ion channels (LGICs) have demonstrated a plausible site of anesthetic action within their transmembrane domains. Although there is a consensus that the transmembrane domain is formed from four membrane-spanning segments, the secondary structure of these segments is not known. We utilized 10 state-of-the-art bioinformatics techniques to predict the transmembrane topology of the tetrameric regions within six members of the LGIC family that are relevant to anesthetic action. They are the human forms of the GABA alpha 1 receptor, the glycine alpha 1 receptor, the 5HT3 serotonin receptor, the nicotinic AChR alpha 4 and alpha 7 receptors and the Torpedo nAChR alpha 1 receptor. The algorithms utilized were HMMTOP, TMHMM, TMPred, PHDhtm, DAS, TMFinder, SOSUI, TMAP, MEMSAT and TOPPred2. The resulting predictions were superimposed on to a multiple sequence alignment of the six amino acid sequences created using the CLUSTAL W algorithm. There was a clear statistical consensus for the presence of four alpha helices in those regions experimentally thought to span the membrane. The consensus of 10 topology prediction techniques supports the hypothesis that the transmembrane subunits of the LGICs are tetrameric bundles of alpha helices.

New Contemporary Criterion-Referenced Assessment Instruments for Astronomy & Geology: TOAST & EGGS

NASA Astrophysics Data System (ADS)

Guffey, Sarah Katie; Slater, Stephanie J.; Slater, Timothy F.

2015-08-01

Considerable effort in the astronomy and Earth sciences education research over the past decade has focused on developing assessment tools in the form of multiple-choice conceptual diagnostics and content knowledge surveys. This has been critically important in advancing discipline-based education research allowing scholar to establish the initial, incoming knowledge state of students as well as to attempt to measure some of the impacts of innovative instructional interventions. Before now, few of the existing instruments were constructed upon a solid list of clearly articulated and widely agreed upon learning objectives. Whereas first-generation assessment tools, such as the Astronomy Diagnostics Test ADT2) were based primarily upon further identifying documented astronomy misconceptions, scholars from the CAPER Center for Astronomy & Physics Education Research team are creating contemporary instruments based instead by developing items using modern test construction techniques and tightly aligned to the consensus learning goals identified by the American Association of the Advancement of Science’s Project 2061 Benchmarks, and the National Research Council’s National Science Education Standards, and the National Research Council’s Frameworks for A Framework for K-12 Science Education: Practices, Crosscutting Concepts, and Core Ideas. These consensus learning goals are further enhanced guiding documents from the American Astronomical Society - Chair’s Conference on ASTRO 101 and the NSF-funded Earth Science Literacy Initiative. Two of the resulting criterion-referenced assessment tools widely used by researchers are the Test Of Astronomy STandards (TOAST) and the Exam of GeoloGy StandardS (EGGS). These easy-to-use and easy-to-score multiple-choice instruments have a high degree of reliability and validity for instructors and researchers needing information on students’ initial knowledge state at the beginning of a course and can be used, in aggregate, to help measure the impact teaching innovations with learning goals tightly aligned to consensus goals of the broader education community.

Customisation of the exome data analysis pipeline using a combinatorial approach.

PubMed

Pattnaik, Swetansu; Vaidyanathan, Srividya; Pooja, Durgad G; Deepak, Sa; Panda, Binay

2012-01-01

The advent of next generation sequencing (NGS) technologies have revolutionised the way biologists produce, analyse and interpret data. Although NGS platforms provide a cost-effective way to discover genome-wide variants from a single experiment, variants discovered by NGS need follow up validation due to the high error rates associated with various sequencing chemistries. Recently, whole exome sequencing has been proposed as an affordable option compared to whole genome runs but it still requires follow up validation of all the novel exomic variants. Customarily, a consensus approach is used to overcome the systematic errors inherent to the sequencing technology, alignment and post alignment variant detection algorithms. However, the aforementioned approach warrants the use of multiple sequencing chemistry, multiple alignment tools, multiple variant callers which may not be viable in terms of time and money for individual investigators with limited informatics know-how. Biologists often lack the requisite training to deal with the huge amount of data produced by NGS runs and face difficulty in choosing from the list of freely available analytical tools for NGS data analysis. Hence, there is a need to customise the NGS data analysis pipeline to preferentially retain true variants by minimising the incidence of false positives and make the choice of right analytical tools easier. To this end, we have sampled different freely available tools used at the alignment and post alignment stage suggesting the use of the most suitable combination determined by a simple framework of pre-existing metrics to create significant datasets.

Primary progressive aphasia: classification of variants in 100 consecutive Brazilian cases

PubMed Central

Senaha, Mirna Lie Hosogi; Caramelli, Paulo; Brucki, Sonia M.D.; Smid, Jerusa; Takada, Leonel T.; Porto, Claudia S.; César, Karolina G.; Matioli, Maria Niures P.; Soares, Roger T.; Mansur, Letícia L.; Nitrini, Ricardo

2013-01-01

Primary progressive aphasia (PPA) is a neurodegenerative clinical syndrome characterized primarily by progressive language impairment. Recently, consensus diagnostic criteria were published for the diagnosis and classification of variants of PPA. The currently recognized variants are nonfluent/agrammatic (PPA-G), logopenic (PPA-L) and semantic (PPA-S). OBJECTIVE To analyze the demographic data and the clinical classification of 100 PPA cases. METHODS Data from 100 PPA patients who were consecutively evaluated between 1999 and 2012 were analyzed. The patients underwent neurological, cognitive and language evaluation. The cases were classified according to the proposed variants, using predominantly the guidelines proposed in the consensus diagnostic criteria from 2011. RESULTS The sample consisted of 57 women and 43 men, aged at onset 67.2±8.1 years (range of between 53 and 83 years). Thirty-five patients presented PPA-S, 29 PPA-G and 16 PPA-L. It was not possible to classify 20% of the cases into any one of the proposed variants. CONCLUSION It was possible to classify 80% of the sample into one of the three PPA variants proposed. Perhaps the consensus classification requires some adjustments to accommodate cases that do not fit into any of the variants and to avoid overlap where cases fit more than one variant. Nonetheless, the established current guidelines are a useful tool to address the classification and diagnosis of PPA and are also of great value in standardizing terminologies to improve consistency across studies from different research centers. PMID:29213827

The American Society of Shoulder and Elbow Therapists' consensus statement on rehabilitation following arthroscopic rotator cuff repair.

PubMed

Thigpen, Charles A; Shaffer, Michael A; Gaunt, Bryce W; Leggin, Brian G; Williams, Gerald R; Wilcox, Reg B

2016-04-01

This is a consensus statement on rehabilitation developed by the American Society of Shoulder and Elbow Therapists. The purpose of this statement is to aid clinical decision making during the rehabilitation of patients after arthroscopic rotator cuff repair. The overarching philosophy of rehabilitation is centered on the principle of the gradual application of controlled stresses to the healing rotator cuff repair with consideration of rotator cuff tear size, tissue quality, and patient variables. This statement describes a rehabilitation framework that includes a 2-week period of strict immobilization and a staged introduction of protected, passive range of motion during weeks 2-6 postoperatively, followed by restoration of active range of motion, and then progressive strengthening beginning at postoperative week 12. When appropriate, rehabilitation continues with a functional progression for return to athletic or demanding work activities. This document represents the first consensus rehabilitation statement developed by a multidisciplinary society of international rehabilitation professionals specifically for the postoperative care of patients after arthroscopic rotator cuff repair. Copyright © 2016 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

Investigating the Role of Accuracy and Self-Correction in the Progress of Struggling First-Grade Readers Participating in a Literacy Intervention

ERIC Educational Resources Information Center

Kelly, Robert H.

2017-01-01

Despite almost a century of research, there is little consensus among researchers and educators about the role of oral reading accuracy in beginning reading progress of struggling readers. Should, for example, students be given easy books to read with high levels of accuracy to promote early reading development or does reading hard texts with…

Apraxia of Speech and Phonological Errors in the Diagnosis of Nonfluent/Agrammatic and Logopenic Variants of Primary Progressive Aphasia

ERIC Educational Resources Information Center

Croot, Karen; Ballard, Kirrie; Leyton, Cristian E.; Hodges, John R.

2012-01-01

Purpose: The International Consensus Criteria for the diagnosis of primary progressive aphasia (PPA; Gorno-Tempini et al., 2011) propose apraxia of speech (AOS) as 1 of 2 core features of nonfluent/agrammatic PPA and propose phonological errors or absence of motor speech disorder as features of logopenic PPA. We investigated the sensitivity and…

Progressive Education Standards: A Neuroscience Framework

ERIC Educational Resources Information Center

O'Grady, Patty

2011-01-01

This paper proposes a coherent and unique set of 12 standards, adopting a neuroscience framework for biologically based on school reform. This model of educational principles and practices aligns with the long-standing principles and practices of the Progressive Education Movement in the United States and the emerging principles of neuroscience.…

Sequence conservation, HLA-E-Restricted peptide, and best-defined CTL/CD8+ epitopes in gag P24 (capsid) of HIV-1 subtype B

NASA Astrophysics Data System (ADS)

Prasetyo, Afiono Agung; Dharmawan, Ruben; Sari, Yulia; Sariyatun, Ratna

2017-02-01

Human immunodeficiency virus type 1 (HIV-1) remains a cause of global health problem. Continuous studies of HIV-1 genetic and immunological profiles are important to find strategies against the virus. This study aimed to conduct analysis of sequence conservation, HLA-E-restricted peptide, and best-defined CTL/CD8+ epitopes in p24 (capsid) of HIV-1 subtype B worldwide. The p24-coding sequences from 3,557 HIV subtype B isolates were aligned using MUSCLE and analysed. Some highly conserved regions (sequence conservation ≥95%) were observed. Two considerably long series of sequences with conservation of 100% was observed at base 349-356 and 550-557 of p24 (HXB2 numbering). The consensus from all aligned isolates was precisely the same as consensus B in the Los Alamos HIV Database. The HLA-E-restricted peptide in amino acid (aa) 14-22 of HIV-1 p24 (AISPRTLNA) was found in 55.9% (1,987/3,557) of HIV-1 subtype B worldwide. Forty-four best-defined CTL/CD8+ epitopes were observed, in which VKNWMTETL epitope (aa 181-189 of p24) restricted by B*4801 was the most frequent, as found in 94.9% of isolates. The results of this study would contribute information about HIV-1 subtype B and benefits for further works willing to develop diagnostic and therapeutic strategies against the virus.

Mapping the yeast genome by melting in nanofluidic devices

NASA Astrophysics Data System (ADS)

Welch, Robert L.; Czolkos, Ilja; Sladek, Rob; Reisner, Walter

2012-02-01

Optical mapping of DNA provides large-scale genomic information that can be used to assemble contigs from next-generation sequencing, and to detect re-arrangements between single cells. A recent optical mapping technique called denaturation mapping has the unique advantage of using physical principles rather than the action of enzymes to probe genomic structure. The absence of reagents or reaction steps makes denaturation mapping simpler than other protocols. Denaturation mapping uses fluorescence microscopy to image the pattern of partial melting along a DNA molecule extended in a channel of cross-section ˜100nm at the heart of a nanofluidic device. We successfully aligned melting maps from single DNA molecules to a theoretical map of the yeast genome (11.6Mbp) to identify their location. By aligning hundreds of molecules we assembled a consensus melting map of the yeast genome with 95% coverage.

On the relationship between tumour growth rate and survival in non-small cell lung cancer.

PubMed

Mistry, Hitesh B

2017-01-01

A recurrent question within oncology drug development is predicting phase III outcome for a new treatment using early clinical data. One approach to tackle this problem has been to derive metrics from mathematical models that describe tumour size dynamics termed re-growth rate and time to tumour re-growth. They have shown to be strong predictors of overall survival in numerous studies but there is debate about how these metrics are derived and if they are more predictive than empirical end-points. This work explores the issues raised in using model-derived metric as predictors for survival analyses. Re-growth rate and time to tumour re-growth were calculated for three large clinical studies by forward and reverse alignment. The latter involves re-aligning patients to their time of progression. Hence, it accounts for the time taken to estimate re-growth rate and time to tumour re-growth but also assesses if these predictors correlate to survival from the time of progression. I found that neither re-growth rate nor time to tumour re-growth correlated to survival using reverse alignment. This suggests that the dynamics of tumours up until disease progression has no relationship to survival post progression. For prediction of a phase III trial I found the metrics performed no better than empirical end-points. These results highlight that care must be taken when relating dynamics of tumour imaging to survival and that bench-marking new approaches to existing ones is essential.

Expert consensus on acute exacerbation of chronic obstructive pulmonary disease in the People’s Republic of China

PubMed Central

Cai, Bai-qiang; Cai, Shao-xi; Chen, Rong-chang; Cui, Li-ying; Feng, Yu-lin; Gu, Yu-tong; Huang, Shao-guang; Liu, Rong-yu; Liu, Guang-nan; Shi, Huan-zhong; Shi, Yi; Song, Yuan-lin; Sun, Tie-ying; Wang, Chang-zheng; Wang, Jing-lan; Wen, Fu-qiang; Xiao, Wei; Xu, Yong-jian; Yan, Xi-xin; Yao, Wan-zhen; Yu, Qin; Zhang, Jing; Zheng, Jin-ping; Liu, Jie; Bai, Chun-xue

2014-01-01

Chronic obstructive pulmonary disease (COPD) is a common disease that severely threatens human health. Acute exacerbation of COPD (AECOPD) is a major cause of disease progression and death, and causes huge medical expenditures. This consensus statement represents a description of clinical features of AECOPD in the People’s Republic of China and a set of recommendations. It is intended to provide clinical guidelines for community physicians, pulmonologists and other health care providers for the prevention, diagnosis, and treatment of AECOPD. PMID:24812503

Clinically meaningful parameters of progression and long-term outcome of Parkinson disease: An international consensus statement.

PubMed

Puschmann, Andreas; Brighina, Laura; Markopoulou, Katerina; Aasly, Jan; Chung, Sun Ju; Frigerio, Roberta; Hadjigeorgiou, Georgios; Kõks, Sulev; Krüger, Rejko; Siuda, Joanna; Wider, Christian; Zesiewicz, Theresa A; Maraganore, Demetrius M

2015-07-01

Parkinson disease (PD) is associated with a clinical course of variable duration, severity, and a combination of motor and non-motor features. Recent PD research has focused primarily on etiology rather than clinical progression and long-term outcomes. For the PD patient, caregivers, and clinicians, information on expected clinical progression and long-term outcomes is of great importance. Today, it remains largely unknown what factors influence long-term clinical progression and outcomes in PD; recent data indicate that the factors that increase the risk to develop PD differ, at least partly, from those that accelerate clinical progression and lead to worse outcomes. Prospective studies will be required to identify factors that influence progression and outcome. We suggest that data for such studies is collected during routine office visits in order to guarantee high external validity of such research. We report here the results of a consensus meeting of international movement disorder experts from the Genetic Epidemiology of Parkinson's Disease (GEO-PD) consortium, who convened to define which long-term outcomes are of interest to patients, caregivers and clinicians, and what is presently known about environmental or genetic factors influencing clinical progression or long-term outcomes in PD. We propose a panel of rating scales that collects a significant amount of phenotypic information, can be performed in the routine office visit and allows international standardization. Research into the progression and long-term outcomes of PD aims at providing individual prognostic information early, adapting treatment choices, and taking specific measures to provide care optimized to the individual patient's needs. Copyright © 2015 Elsevier Ltd. All rights reserved.

Identifying key performance indicators for nursing and midwifery care using a consensus approach.

PubMed

McCance, Tanya; Telford, Lorna; Wilson, Julie; Macleod, Olive; Dowd, Audrey

2012-04-01

The aim of this study was to gain consensus on key performance indicators that are appropriate and relevant for nursing and midwifery practice in the current policy context. There is continuing demand to demonstrate effectiveness and efficiency in health and social care and to communicate this at boardroom level. Whilst there is substantial literature on the use of clinical indicators and nursing metrics, there is less evidence relating to indicators that reflect the patient experience. A consensus approach was used to identify relevant key performance indicators. A nominal group technique was used comprising two stages: a workshop involving all grades of nursing and midwifery staff in two HSC trusts in Northern Ireland (n = 50); followed by a regional Consensus Conference (n = 80). During the workshop, potential key performance indicators were identified. This was used as the basis for the Consensus Conference, which involved two rounds of consensus. Analysis was based on aggregated scores that were then ranked. Stage one identified 38 potential indicators and stage two prioritised the eight top-ranked indicators as a core set for nursing and midwifery. The relevance and appropriateness of these indicators were confirmed with nurses and midwives working in a range of settings and from the perspective of service users. The eight indicators identified do not conform to the majority of other nursing metrics generally reported in the literature. Furthermore, they are strategically aligned to work on the patient experience and are reflective of the fundamentals of nursing and midwifery practice, with the focus on person-centred care. Nurses and midwives have a significant contribution to make in determining the extent to which these indicators are achieved in practice. Furthermore, measurement of such indicators provides an opportunity to evidence of the unique impact of nursing/midwifery care on the patient experience. © 2011 Blackwell Publishing Ltd.

Time for change: a roadmap to guide the implementation of the World Anti-Doping Code 2015

PubMed Central

Dvorak, Jiri; Baume, Norbert; Botré, Francesco; Broséus, Julian; Budgett, Richard; Frey, Walter O; Geyer, Hans; Harcourt, Peter Rex; Ho, Dave; Howman, David; Isola, Victor; Lundby, Carsten; Marclay, François; Peytavin, Annie; Pipe, Andrew; Pitsiladis, Yannis P; Reichel, Christian; Robinson, Neil; Rodchenkov, Grigory; Saugy, Martial; Sayegh, Souheil; Segura, Jordi; Thevis, Mario; Vernec, Alan; Viret, Marjolaine; Vouillamoz, Marc; Zorzoli, Mario

2014-01-01

A medical and scientific multidisciplinary consensus meeting was held from 29 to 30 November 2013 on Anti-Doping in Sport at the Home of FIFA in Zurich, Switzerland, to create a roadmap for the implementation of the 2015 World Anti-Doping Code. The consensus statement and accompanying papers set out the priorities for the antidoping community in research, science and medicine. The participants achieved consensus on a strategy for the implementation of the 2015 World Anti-Doping Code. Key components of this strategy include: (1) sport-specific risk assessment, (2) prevalence measurement, (3) sport-specific test distribution plans, (4) storage and reanalysis, (5) analytical challenges, (6) forensic intelligence, (7) psychological approach to optimise the most deterrent effect, (8) the Athlete Biological Passport (ABP) and confounding factors, (9) data management system (Anti-Doping Administration & Management System (ADAMS), (10) education, (11) research needs and necessary advances, (12) inadvertent doping and (13) management and ethics: biological data. True implementation of the 2015 World Anti-Doping Code will depend largely on the ability to align thinking around these core concepts and strategies. FIFA, jointly with all other engaged International Federations of sports (Ifs), the International Olympic Committee (IOC) and World Anti-Doping Agency (WADA), are ideally placed to lead transformational change with the unwavering support of the wider antidoping community. The outcome of the consensus meeting was the creation of the ad hoc Working Group charged with the responsibility of moving this agenda forward. PMID:24764550

Time for change: a roadmap to guide the implementation of the World Anti-Doping Code 2015.

PubMed

Dvorak, Jiri; Baume, Norbert; Botré, Francesco; Broséus, Julian; Budgett, Richard; Frey, Walter O; Geyer, Hans; Harcourt, Peter Rex; Ho, Dave; Howman, David; Isola, Victor; Lundby, Carsten; Marclay, François; Peytavin, Annie; Pipe, Andrew; Pitsiladis, Yannis P; Reichel, Christian; Robinson, Neil; Rodchenkov, Grigory; Saugy, Martial; Sayegh, Souheil; Segura, Jordi; Thevis, Mario; Vernec, Alan; Viret, Marjolaine; Vouillamoz, Marc; Zorzoli, Mario

2014-05-01

A medical and scientific multidisciplinary consensus meeting was held from 29 to 30 November 2013 on Anti-Doping in Sport at the Home of FIFA in Zurich, Switzerland, to create a roadmap for the implementation of the 2015 World Anti-Doping Code. The consensus statement and accompanying papers set out the priorities for the antidoping community in research, science and medicine. The participants achieved consensus on a strategy for the implementation of the 2015 World Anti-Doping Code. Key components of this strategy include: (1) sport-specific risk assessment, (2) prevalence measurement, (3) sport-specific test distribution plans, (4) storage and reanalysis, (5) analytical challenges, (6) forensic intelligence, (7) psychological approach to optimise the most deterrent effect, (8) the Athlete Biological Passport (ABP) and confounding factors, (9) data management system (Anti-Doping Administration & Management System (ADAMS), (10) education, (11) research needs and necessary advances, (12) inadvertent doping and (13) management and ethics: biological data. True implementation of the 2015 World Anti-Doping Code will depend largely on the ability to align thinking around these core concepts and strategies. FIFA, jointly with all other engaged International Federations of sports (Ifs), the International Olympic Committee (IOC) and World Anti-Doping Agency (WADA), are ideally placed to lead transformational change with the unwavering support of the wider antidoping community. The outcome of the consensus meeting was the creation of the ad hoc Working Group charged with the responsibility of moving this agenda forward.

Mounting and Alignment of IXO Mirror Segments

NASA Technical Reports Server (NTRS)

Chan, Kai-Wing; Zhang, William; Evans, Tyler; McClelland, Ryan; Hong, Melinda; Mazzarella, James; Saha, Timo; Jalota, Lalit; Olsen, Lawrence; Byron, Glenn

2010-01-01

A suspension-mounting scheme is developed for the IXO (International X-ray Observatory) mirror segments in which the figure of the mirror segment is preserved in each stage of mounting. The mirror, first fixed on a thermally compatible strongback, is subsequently transported, aligned and transferred onto its mirror housing. In this paper, we shall outline the requirement, approaches, and recent progress of the suspension mount processes.

Patellofemoral Osteoarthritis Progression and Alignment Changes after Open-Wedge High Tibial Osteotomy Do Not Affect Clinical Outcomes at Mid-term Follow-up.

PubMed

Goshima, Kenichi; Sawaguchi, Takeshi; Shigemoto, Kenji; Iwai, Shintaro; Nakanishi, Akira; Ueoka, Ken

2017-10-01

To evaluate the clinical and radiological outcomes of open-wedge high tibial osteotomy (OWHTO) with respect to the patellofemoral joint and to assess whether patellofemoral osteoarthritis (OA) progression and alignment changes after OWHTO affect clinical outcomes. Inclusion criteria were consecutive patients who underwent OWHTO from March 2005 to September 2013. Exclusion criteria were loss to follow-up within 2 years and absence of second-look arthroscopy findings at the time of plate removal. The clinical parameters, including anterior knee pain while climbing stairs, Japanese Orthopedic Association score, and Oxford Knee Score, were evaluated. Radiological outcomes, including weight-bearing line ratio, modified Blackburne-Peel ratio, posterior tibial slope, tilting angle, lateral shift ratio, and patellofemoral OA (Kellgren-Lawrence grade), were evaluated preoperatively and at the final follow-up. Cartilage status (International Cartilage Repair Society grade) was evaluated at the initial HTO and at plate removal. Fifty-three patients (60 knees) were included in this study. The mean follow-up was 58.2 ± 22.4 months. Two knees (3%) presented with mild anterior knee pain after OWHTO. The mean Japanese Orthopedic Association score (66.9 ± 11.2 to 91.2 ± 9.7) significantly improved (P < .001), and the mean Oxford Knee Score at the final follow-up was 42.0 ± 5.3. The mean modified Blackburne-Peel ratio (0.9 ± 0.1 to 0.7 ± 0.1, P < .001) and tilting angle (6.8 ± 3.7 to 5.6 ± 3.4, P = .033) significantly decreased after OWHTO, whereas no significant changes in posterior tibial slope (P = .511) and lateral shift ratio (P = .522) were observed. Radiologically, patellofemoral OA had progressed in 15 knees (27%), and arthroscopically patellofemoral cartilage degeneration had progressed in 27 knees (45%). However, there was no significant correlation between changes in patellofemoral alignment and clinical outcomes. Changes in patellofemoral alignment and patellofemoral OA progression did not affect the clinical outcomes of OWHTO at mid-term follow-up. Level IV, therapeutic case series. Copyright © 2017 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

Consensus statement for diagnosis of subcortical small vessel disease

PubMed Central

Wallin, Anders; Wardlaw, Joanna M; Markus, Hugh S; Montaner, Joan; Wolfson, Leslie; Iadecola, Costantino; Zlokovic, Berislav V; Joutel, Anne; Dichgans, Martin; Duering, Marco; Schmidt, Reinhold; Korczyn, Amos D; Grinberg, Lea T; Chui, Helena C; Hachinski, Vladimir

2016-01-01

Vascular cognitive impairment (VCI) is the diagnostic term used to describe a heterogeneous group of sporadic and hereditary diseases of the large and small blood vessels. Subcortical small vessel disease (SVD) leads to lacunar infarcts and progressive damage to the white matter. Patients with progressive damage to the white matter, referred to as Binswanger’s disease (BD), constitute a spectrum from pure vascular disease to a mixture with neurodegenerative changes. Binswanger’s disease patients are a relatively homogeneous subgroup with hypoxic hypoperfusion, lacunar infarcts, and inflammation that act synergistically to disrupt the blood–brain barrier (BBB) and break down myelin. Identification of this subgroup can be facilitated by multimodal disease markers obtained from clinical, cerebrospinal fluid, neuropsychological, and imaging studies. This consensus statement identifies a potential set of biomarkers based on underlying pathologic changes that could facilitate diagnosis and aid patient selection for future collaborative treatment trials. PMID:26198175

The PULSE Vision & Change Rubrics, Version 1.0: A Valid and Equitable Tool to Measure Transformation of Life Sciences Departments at All Institution Types

PubMed Central

Brancaccio-Taras, Loretta; Pape-Lindstrom, Pamela; Peteroy-Kelly, Marcy; Aguirre, Karen; Awong-Taylor, Judy; Balser, Teri; Cahill, Michael J.; Frey, Regina F.; Jack, Thomas; Kelrick, Michael; Marley, Kate; Miller, Kathryn G.; Osgood, Marcy; Romano, Sandra; Uzman, J. Akif; Zhao, Jiuqing

2016-01-01

The PULSE Vision & Change Rubrics, version 1.0, assess life sciences departments’ progress toward implementation of the principles of the Vision and Change report. This paper reports on the development of the rubrics, their validation, and their reliability in measuring departmental change aligned with the Vision and Change recommendations. The rubrics assess 66 different criteria across five areas: Curriculum Alignment, Assessment, Faculty Practice/Faculty Support, Infrastructure, and Climate for Change. The results from this work demonstrate the rubrics can be used to evaluate departmental transformation equitably across institution types and represent baseline data about the adoption of the Vision and Change recommendations by life sciences programs across the United States. While all institution types have made progress, liberal arts institutions are farther along in implementing these recommendations. Generally, institutions earned the highest scores on the Curriculum Alignment rubric and the lowest scores on the Assessment rubric. The results of this study clearly indicate that the Vision & Change Rubrics, version 1.0, are valid and equitable and can track long-term progress of the transformation of life sciences departments. In addition, four of the five rubrics have broad applicability and can be used to evaluate departmental transformation by other science, technology, engineering, and mathematics disciplines. PMID:27856548

Laboratory simulation of field-aligned currents

NASA Technical Reports Server (NTRS)

Wessel, Frank J.; Rostoker, Norman

1993-01-01

A summary of progress during the period Apr. 1992 to Mar. 1993 is provided. Objectives of the research are (1) to simulate, via laboratory experiments, the three terms of the field-aligned current equation; (2) to simulate auroral-arc formation processes by configuring the boundary conditions of the experimental chamber and plasma parameters to produce highly localized return currents at the end of a field-aligned current system; and (3) to extrapolate these results, using theoretical and computational techniques, to the problem of magnetospheric-ionospheric coupling and to compare them with published literature signatures of auroral-arc phenomena.

Bedtime misalignment and progression of breast cancer.

PubMed

Hahm, Bong-Jin; Jo, Booil; Dhabhar, Firdaus S; Palesh, Oxana; Aldridge-Gerry, Arianna; Bajestan, Sepideh N; Neri, Eric; Nouriani, Bita; Spiegel, David; Zeitzer, Jamie M

2014-03-01

Disruption of circadian rhythms, which frequently occurs during night shift work, may be associated with cancer progression. The effect of chronotype (preference for behaviors such as sleep, work, or exercise to occur at particular times of day, with an associated difference in circadian physiology) and alignment of bedtime (preferred vs. habitual), however, have not yet been studied in the context of cancer progression in women with breast cancer. Chronotype and alignment of actual bedtime with preferred chronotype were examined using the Morningness-Eveningness Scale (MEQ) and sleep-wake log among 85 women with metastatic breast cancer. Their association with disease-free interval (DFI) was retrospectively examined using the Cox proportional hazards model. Median DFI was 81.9 months for women with aligned bedtimes ("going to bed at preferred bedtime") (n = 72), and 46.9 months for women with misaligned bedtimes ("going to bed later or earlier than the preferred bedtime") (n = 13) (log rank p = 0.001). In a multivariate Cox proportional hazard model, after controlling for other significant predictors of DFI, including chronotype (morning type/longer DFI; HR = 0.539, 95% CI = 0.320-0.906, p = 0.021), estrogen receptor (ER) status at initial diagnosis (negative/shorter DFI; HR = 2.169, 95% CI = 1.124-4.187, p = 0.028) and level of natural-killer cell count (lower levels/shorter DFI; HR = 1.641, 95% CI = 1.000-2.695, p = 0.050), misaligned bedtimes was associated with shorter DFI, compared to aligned bedtimes (HR = 3.180, 95% CI = 1.327-7.616, p = 0.018). Our data indicate that a misalignment of bedtime on a daily basis, an indication of circadian disruption, is associated with more rapid breast cancer progression as measured by DFI. Considering the limitations of small sample size and study design, a prospective study with a larger sample is necessary to explore their causal relationship and underlying mechanisms.

Phylogenetic study of Class Armophorea (Alveolata, Ciliophora) based on 18S-rDNA data.

PubMed

da Silva Paiva, Thiago; do Nascimento Borges, Bárbara; da Silva-Neto, Inácio Domingos

2013-12-01

The 18S rDNA phylogeny of Class Armophorea, a group of anaerobic ciliates, is proposed based on an analysis of 44 sequences (out of 195) retrieved from the NCBI/GenBank database. Emphasis was placed on the use of two nucleotide alignment criteria that involved variation in the gap-opening and gap-extension parameters and the use of rRNA secondary structure to orientate multiple-alignment. A sensitivity analysis of 76 data sets was run to assess the effect of variations in indel parameters on tree topologies. Bayesian inference, maximum likelihood and maximum parsimony phylogenetic analyses were used to explore how different analytic frameworks influenced the resulting hypotheses. A sensitivity analysis revealed that the relationships among higher taxa of the Intramacronucleata were dependent upon how indels were determined during multiple-alignment of nucleotides. The phylogenetic analyses rejected the monophyly of the Armophorea most of the time and consistently indicated that the Metopidae and Nyctotheridae were related to the Litostomatea. There was no consensus on the placement of the Caenomorphidae, which could be a sister group of the Metopidae + Nyctorheridae, or could have diverged at the base of the Spirotrichea branch or the Intramacronucleata tree.

Phylogenetic study of Class Armophorea (Alveolata, Ciliophora) based on 18S-rDNA data

PubMed Central

da Silva Paiva, Thiago; do Nascimento Borges, Bárbara; da Silva-Neto, Inácio Domingos

2013-01-01

The 18S rDNA phylogeny of Class Armophorea, a group of anaerobic ciliates, is proposed based on an analysis of 44 sequences (out of 195) retrieved from the NCBI/GenBank database. Emphasis was placed on the use of two nucleotide alignment criteria that involved variation in the gap-opening and gap-extension parameters and the use of rRNA secondary structure to orientate multiple-alignment. A sensitivity analysis of 76 data sets was run to assess the effect of variations in indel parameters on tree topologies. Bayesian inference, maximum likelihood and maximum parsimony phylogenetic analyses were used to explore how different analytic frameworks influenced the resulting hypotheses. A sensitivity analysis revealed that the relationships among higher taxa of the Intramacronucleata were dependent upon how indels were determined during multiple-alignment of nucleotides. The phylogenetic analyses rejected the monophyly of the Armophorea most of the time and consistently indicated that the Metopidae and Nyctotheridae were related to the Litostomatea. There was no consensus on the placement of the Caenomorphidae, which could be a sister group of the Metopidae + Nyctorheridae, or could have diverged at the base of the Spirotrichea branch or the Intramacronucleata tree. PMID:24385862

Physician-Hospital Alignment in Orthopedic Surgery.

PubMed

Bushnell, Brandon D

2015-09-01

The concept of "alignment" between physicians and hospitals is a popular buzzword in the age of health care reform. Despite their often tumultuous histories, physicians and hospitals find themselves under increasing pressures to work together toward common goals. However, effective alignment is more than just simple cooperation between parties. The process of achieving alignment does not have simple, universal steps. Alignment will differ based on individual situational factors and the type of specialty involved. Ultimately, however, there are principles that underlie the concept of alignment and should be a part of any physician-hospital alignment efforts. In orthopedic surgery, alignment involves the clinical, administrative, financial, and even personal aspects of a surgeon's practice. It must be based on the principles of financial interest, clinical authority, administrative participation, transparency, focus on the patient, and mutual necessity. Alignment can take on various forms as well, with popular models consisting of shared governance and comanagement, gainsharing, bundled payments, accountable care organizations, and other methods. As regulatory and financial pressures continue to motivate physicians and hospitals to develop alignment relationships, new and innovative methods of alignment will also appear. Existing models will mature and evolve, with individual variability based on local factors. However, certain trends seem to be appearing as time progresses and alignment relationships deepen, including regional and national collaboration, population management, and changes in the legal system. This article explores the history, principles, and specific methods of physician-hospital alignment and its critical importance for the future of health care delivery. Copyright 2015, SLACK Incorporated.

Straight A's: Public Education Policy and Progress. Volume 11, Number 9

ERIC Educational Resources Information Center

Amos, Jason, Ed.

2011-01-01

"Straight A's: Public Education Policy and Progress" is a biweekly newsletter that focuses on education news and events both in Washington, DC and around the country. The following articles are included in this issue: (1) "Engineering Solutions to the National Crisis in Literacy": Alliance Brief Calls for Alignment Between…

From Theory to Data: The Process of Refining Learning Progressions

ERIC Educational Resources Information Center

Shea, Nicole A.; Duncan, Ravit Golan

2013-01-01

Learning progressions (LPs) are theoretical models of how learners develop expertise in a domain over extended periods of time. Recent policy reports have touted LPs as a promising approach to aligning standards, curriculum, and assessment. However, the scholarship on LPs is relatively sparse, and the jury is still out on the theoretical and…

Staying True?: Progressive Leadership in Tough Times

ERIC Educational Resources Information Center

Pignatelli, Frank

2012-01-01

A system of accountability in public schools predicated upon standardized testing accompanied by high-stakes consequences for leaders, as well as teachers and students, has posed a daunting challenge to educational leaders who align themselves with core tenets of progressive education. This essay explores what it might mean--and take--to stay true…

SWPhylo - A Novel Tool for Phylogenomic Inferences by Comparison of Oligonucleotide Patterns and Integration of Genome-Based and Gene-Based Phylogenetic Trees.

PubMed

Yu, Xiaoyu; Reva, Oleg N

2018-01-01

Modern phylogenetic studies may benefit from the analysis of complete genome sequences of various microorganisms. Evolutionary inferences based on genome-scale analysis are believed to be more accurate than the gene-based alternative. However, the computational complexity of current phylogenomic procedures, inappropriateness of standard phylogenetic tools to process genome-wide data, and lack of reliable substitution models which correlates with alignment-free phylogenomic approaches deter microbiologists from using these opportunities. For example, the super-matrix and super-tree approaches of phylogenomics use multiple integrated genomic loci or individual gene-based trees to infer an overall consensus tree. However, these approaches potentially multiply errors of gene annotation and sequence alignment not mentioning the computational complexity and laboriousness of the methods. In this article, we demonstrate that the annotation- and alignment-free comparison of genome-wide tetranucleotide frequencies, termed oligonucleotide usage patterns (OUPs), allowed a fast and reliable inference of phylogenetic trees. These were congruent to the corresponding whole genome super-matrix trees in terms of tree topology when compared with other known approaches including 16S ribosomal RNA and GyrA protein sequence comparison, complete genome-based MAUVE, and CVTree methods. A Web-based program to perform the alignment-free OUP-based phylogenomic inferences was implemented at http://swphylo.bi.up.ac.za/. Applicability of the tool was tested on different taxa from subspecies to intergeneric levels. Distinguishing between closely related taxonomic units may be enforced by providing the program with alignments of marker protein sequences, eg, GyrA.

SWPhylo – A Novel Tool for Phylogenomic Inferences by Comparison of Oligonucleotide Patterns and Integration of Genome-Based and Gene-Based Phylogenetic Trees

PubMed Central

Yu, Xiaoyu; Reva, Oleg N

2018-01-01

Modern phylogenetic studies may benefit from the analysis of complete genome sequences of various microorganisms. Evolutionary inferences based on genome-scale analysis are believed to be more accurate than the gene-based alternative. However, the computational complexity of current phylogenomic procedures, inappropriateness of standard phylogenetic tools to process genome-wide data, and lack of reliable substitution models which correlates with alignment-free phylogenomic approaches deter microbiologists from using these opportunities. For example, the super-matrix and super-tree approaches of phylogenomics use multiple integrated genomic loci or individual gene-based trees to infer an overall consensus tree. However, these approaches potentially multiply errors of gene annotation and sequence alignment not mentioning the computational complexity and laboriousness of the methods. In this article, we demonstrate that the annotation- and alignment-free comparison of genome-wide tetranucleotide frequencies, termed oligonucleotide usage patterns (OUPs), allowed a fast and reliable inference of phylogenetic trees. These were congruent to the corresponding whole genome super-matrix trees in terms of tree topology when compared with other known approaches including 16S ribosomal RNA and GyrA protein sequence comparison, complete genome-based MAUVE, and CVTree methods. A Web-based program to perform the alignment-free OUP-based phylogenomic inferences was implemented at http://swphylo.bi.up.ac.za/. Applicability of the tool was tested on different taxa from subspecies to intergeneric levels. Distinguishing between closely related taxonomic units may be enforced by providing the program with alignments of marker protein sequences, eg, GyrA. PMID:29511354

SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction.

PubMed

Hagopian, Raffi; Davidson, John R; Datta, Ruchira S; Samad, Bushra; Jarvis, Glen R; Sjölander, Kimmen

2010-07-01

We present the jump-start simultaneous alignment and tree construction using hidden Markov models (SATCHMO-JS) web server for simultaneous estimation of protein multiple sequence alignments (MSAs) and phylogenetic trees. The server takes as input a set of sequences in FASTA format, and outputs a phylogenetic tree and MSA; these can be viewed online or downloaded from the website. SATCHMO-JS is an extension of the SATCHMO algorithm, and employs a divide-and-conquer strategy to jump-start SATCHMO at a higher point in the phylogenetic tree, reducing the computational complexity of the progressive all-versus-all HMM-HMM scoring and alignment. Results on a benchmark dataset of 983 structurally aligned pairs from the PREFAB benchmark dataset show that SATCHMO-JS provides a statistically significant improvement in alignment accuracy over MUSCLE, Multiple Alignment using Fast Fourier Transform (MAFFT), ClustalW and the original SATCHMO algorithm. The SATCHMO-JS webserver is available at http://phylogenomics.berkeley.edu/satchmo-js. The datasets used in these experiments are available for download at http://phylogenomics.berkeley.edu/satchmo-js/supplementary/.

Society for Immunotherapy of Cancer consensus statement on immunotherapy for the treatment of bladder carcinoma.

PubMed

Kamat, Ashish M; Bellmunt, Joaquim; Galsky, Matthew D; Konety, Badrinath R; Lamm, Donald L; Langham, David; Lee, Cheryl T; Milowsky, Matthew I; O'Donnell, Michael A; O'Donnell, Peter H; Petrylak, Daniel P; Sharma, Padmanee; Skinner, Eila C; Sonpavde, Guru; Taylor, John A; Abraham, Prasanth; Rosenberg, Jonathan E

2017-08-15

The standard of care for most patients with non-muscle-invasive bladder cancer (NMIBC) is immunotherapy with intravesical Bacillus Calmette-Guérin (BCG), which activates the immune system to recognize and destroy malignant cells and has demonstrated durable clinical benefit. Urologic best-practice guidelines and consensus reports have been developed and strengthened based on data on the timing, dose, and duration of therapy from randomized clinical trials, as well as by critical evaluation of criteria for progression. However, these reports have not penetrated the community, and many patients do not receive appropriate therapy. Additionally, several immune checkpoint inhibitors have recently been approved for treatment of metastatic disease. The approval of immune checkpoint blockade for patients with platinum-resistant or -ineligible metastatic bladder cancer has led to considerations of expanded use for both advanced and, potentially, localized disease. To address these issues and others surrounding the appropriate use of immunotherapy for the treatment of bladder cancer, the Society for Immunotherapy of Cancer (SITC) convened a Task Force of experts, including physicians, patient advocates, and nurses, to address issues related to patient selection, toxicity management, clinical endpoints, as well as the combination and sequencing of therapies. Following the standard approach established by the Society for other cancers, a systematic literature review and analysis of data, combined with consensus voting was used to generate guidelines. Here, we provide a consensus statement for the use of immunotherapy in patients with bladder cancer, with plans to update these recommendations as the field progresses.

Nucleotide Sequence of the blaRTG-2 (CARB-5) Gene and Phylogeny of a New Group of Carbenicillinases

PubMed Central

Choury, Daniele; Szajnert, Marie-France; Joly-Guillou, Marie-Laure; Azibi, Kemal; Delpech, Marc; Paul, Gérard

2000-01-01

We determined the nucleotide sequence of the bla gene for the Acinetobacter calcoaceticus β-lactamase previously described as CARB-5. Alignment of the deduced amino acid sequence with those of known β-lactamases revealed that CARB-5 possesses an RTG triad in box VII, as described for the Proteus mirabilis GN79 enzyme, instead of the RSG consensus characteristic of the other carbenicillinases. Phylogenetic studies showed that these RTG enzymes constitute a new, separate group, possibly ancestors of the carbenicillinase family. PMID:10722515

How to Fabricate Functional Artificial Luciferases for Bioassays.

PubMed

Kim, Sung-Bae; Fujii, Rika

2016-01-01

The present protocol introduces fabrication of artificial luciferases (ALuc(®)) by extracting the consensus amino acids from the alignment of copepod luciferase sequences. The made ALucs have unique sequential identities that are phylogenetically distinctive from those of any existing copepod luciferase. Some ALucs exhibited heat stability, and strong and greatly prolonged optical intensities. The made ALucs are applicable to various bioassays as an optical readout, including live cell imaging, single-chain probes, and bioluminescent tags of antibodies. The present protocol guides on how to fabricate a unique artificial luciferase with designed optical properties and functionalities.

MUSCLE: multiple sequence alignment with high accuracy and high throughput.

PubMed

Edgar, Robert C

2004-01-01

We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.

Progress of nanopositioning stages development for hard x-ray nanofocusing and coherence preservation optics at the APS

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

Shu, Deming

2015-07-01

Customized flexure mechanisms and precision thermal expansion compensation are needed for the development of nanopositioning stages for hard x-ray nanofocusing and coherence preservation optics at the APS. Recent progress of such stage development is summarized in this paper, which includes: stages designed for alignment apparatus for K-B mirrors with 20 - 50 nm focal spot; alignment apparatus for six Fresnel zone plates stacking with 20 nm focal spot; stages for switchable multiple nanofocusing system; UHV hard x-ray monochromators for coherence related applications; and four-crystal hard x-ray split-and-delay line with coherence preservation. Preliminary test results for mechanical performance of these nanopositioningmore » stages are also discussed in this paper.« less

Building consensus and partnerships for implementing the MAP-21 section 5310 program in California.

DOT National Transportation Integrated Search

2014-04-01

The Moving Ahead for Progress in the 21st Century Act (MAP-21)the legislation that currently provides funding for federal : transportationallows metropolitan planning organizations (MPOs) or eligible large, urbanized area (UZA) agencies to assu...

Evaluation of service reliability impacts of traffic signal priority strategies for bus transit

DOT National Transportation Integrated Search

2003-03-31

Recent progress in technology has facilitated the design, testing, and deployment of traffic signal priority strategies for transit buses. However, a clear consensus has not emerged regarding the evaluation of these strategies. Each agency implementi...

How I treat bronchiolitis obliterans syndrome after hematopoietic stem cell transplantation.

PubMed

Williams, Kirsten M

2017-01-26

In past years, a diagnosis of bronchiolitis obliterans syndrome (BOS) after allogeneic hematopoietic cell transplant (HCT) conferred nearly universal mortality secondary to lack of consensus for diagnostic criteria, poorly understood disease pathogenesis, and very few studies of therapeutic or supportive care interventions. Recently, however, progress has been made in these areas: revised consensus diagnostic guidelines are now available, supportive care has improved, there is greater understanding of potential mechanisms of disease, and prospective trials are being conducted. This article describes these advances and provides suggestions to optimize therapy for patients with BOS after HCT.

Screening of matrix metalloproteinases available from the protein data bank: insights into biological functions, domain organization, and zinc binding groups.

PubMed

Nicolotti, Orazio; Miscioscia, Teresa Fabiola; Leonetti, Francesco; Muncipinto, Giovanni; Carotti, Angelo

2007-01-01

A total of 142 matrix metalloproteinase (MMP) X-ray crystallographic structures were retrieved from the Protein Data Bank (PDB) and analyzed by an automated and efficient routine, developed in-house, with a series of bioinformatic tools. Highly informative heat maps and hierarchical clusterograms provided a reliable and comprehensive representation of the relationships existing among MMPs, enlarging and complementing the current knowledge in the field. Multiple sequence and structural alignments permitted better location and display of key MMP motifs and quantification of the residue consensus at each amino acid position in the most critical binding subsites of MMPs. The MMP active site consensus sequences, the C-alpha root-mean-square deviation (RMSd) analysis of diverse enzymatic subsites, and the examination of the chemical nature, binding topologies, and zinc binding groups (ZBGs) of ligands extracted from crystallographic complexes provided useful insights on the structural arrangements of the most potent MMP inhibitors.

Innovation in creating a strategic plan for research within an academic community.

PubMed

Best, Kaitlin M; Jarrín, Olga; Buttenheim, Alison M; Bowles, Kathryn H; Curley, Martha A Q

2015-01-01

Strategic planning for research priorities in schools of nursing requires consensus building and engagement of key stakeholders. However, traditional approaches to strategic planning using work groups and committees sometimes result in low rates of faculty participation and fail to engage other important stakeholders. The purpose of this article is to describe the unique low-cost, high-yield processes that contributed to the rapid development of our school's strategic research plan over the course of 1 month. Using the name recognition of the National Collegiate Athletic Association's annual basketball tournament, we were able to encourage high levels of participation by faculty, doctoral students, and postdoctoral fellows in not only developing a consensus around eight broad lines of inquiry but also offering tangible recommendations for accomplishing those goals within the next 5 years. Other schools of nursing seeking to evaluate their research enterprise and align their science with national priorities could easily replicate this approach. Copyright © 2015 Elsevier Inc. All rights reserved.

Composition of a Vision Screen for Servicemembers With Traumatic Brain Injury: Consensus Using a Modified Nominal Group Technique

PubMed Central

Finkelstein, Marsha; Llanos, Imelda; Scheiman, Mitchell; Wagener, Sharon Gowdy

2014-01-01

Vision impairment is common in the first year after traumatic brain injury (TBI), including among service members whose brain injuries occurred during deployment in Iraq and Afghanistan. Occupational therapy practitioners provide routine vision screening to inform treatment planning and referral to vision specialists, but existing methods are lacking because many tests were developed for children and do not screen for vision dysfunction typical of TBI. An expert panel was charged with specifying the composition of a vision screening protocol for servicemembers with TBI. A modified nominal group technique fostered discussion and objective determinations of consensus. After considering 29 vision tests, the panel recommended a nine-test vision screening that examines functional performance, self-reported problems, far–near acuity, reading, accommodation, convergence, eye alignment and binocular vision, saccades, pursuits, and visual fields. Research is needed to develop reliable, valid, and clinically feasible vision screening protocols to identify TBI-related vision disorders in adults. PMID:25005505

Aligning the unalignable: bacteriophage whole genome alignments.

PubMed

Bérard, Sèverine; Chateau, Annie; Pompidor, Nicolas; Guertin, Paul; Bergeron, Anne; Swenson, Krister M

2016-01-13

In recent years, many studies focused on the description and comparison of large sets of related bacteriophage genomes. Due to the peculiar mosaic structure of these genomes, few informative approaches for comparing whole genomes exist: dot plots diagrams give a mostly qualitative assessment of the similarity/dissimilarity between two or more genomes, and clustering techniques are used to classify genomes. Multiple alignments are conspicuously absent from this scene. Indeed, whole genome aligners interpret lack of similarity between sequences as an indication of rearrangements, insertions, or losses. This behavior makes them ill-prepared to align bacteriophage genomes, where even closely related strains can accomplish the same biological function with highly dissimilar sequences. In this paper, we propose a multiple alignment strategy that exploits functional collinearity shared by related strains of bacteriophages, and uses partial orders to capture mosaicism of sets of genomes. As classical alignments do, the computed alignments can be used to predict that genes have the same biological function, even in the absence of detectable similarity. The Alpha aligner implements these ideas in visual interactive displays, and is used to compute several examples of alignments of Staphylococcus aureus and Mycobacterium bacteriophages, involving up to 29 genomes. Using these datasets, we prove that Alpha alignments are at least as good as those computed by standard aligners. Comparison with the progressive Mauve aligner - which implements a partial order strategy, but whose alignments are linearized - shows a greatly improved interactive graphic display, while avoiding misalignments. Multiple alignments of whole bacteriophage genomes work, and will become an important conceptual and visual tool in comparative genomics of sets of related strains. A python implementation of Alpha, along with installation instructions for Ubuntu and OSX, is available on bitbucket (https://bitbucket.org/thekswenson/alpha).

Revisioning a clinical nurse specialist curriculum in 3 specialty tracks.

PubMed

Arslanian-Engoren, Cynthia; Sullivan, Barbara-Jean; Struble, Laura

2011-01-01

The objective of the present study was to revise 3 clinical nurse specialist (CNS) educational tracks with current National Association of Clinical Nurse Specialist core competencies and educational expectations. National curricula recommendations include core competencies by the 3 spheres of influence. Advanced practice registered nurses consensus model educational requirements include a minimum of 500 faculty-supervised clinical hours; separate graduate courses in pharmacology, pathophysiology, and advanced physical assessment; and content in differential diagnosis disease management, decision making, and role preparation. This educational initiative was designed to (1) align with core competencies and advanced practice registered nurse consensus model recommendations, (2) create an innovative learning environment, (3) meet the needs of diverse student populations, (4) align with emerging doctor of nursing practice programs, (5) create a high-efficiency and high-quality environment to manage human and fiscal resources, and (6) reduce duplication of efforts. Courses were revised that did not meet current CNS educational preparation expectations. A total of 11 didactic and clinical sequences courses were developed for the 3 tracks to (1) ensure minimum numbers of clinical hours; (2) expand content on health promotion and risk reduction, advanced practice nurse role, and the healthcare delivery system; (3) consolidate clinical courses; and (4) resequence foundational content before beginning clinical courses. Revisioning a CNS curriculum in 3 specialty tracks is challenging but doable using innovative and creative approaches. The innovative process used to revise our CNS curriculum will assist nurse educators faced with similar program delivery challenges to meet future directions for educating CNS students in advanced nursing practice. Copyright © 2011 Lippincott Williams & Wilkins.

First Results from the Test Of Astronomy STandards (TOAST) Assessment Instrument

NASA Astrophysics Data System (ADS)

Slater, Stephanie

2009-01-01

Considerable effort in the astronomy education research over the past several years has focused on developing assessment tools in the form of multiple-choice conceptual diagnostics and content knowledge surveys. This has been critically important in advancing astronomy as a sub-discipline of physics education research, allowing researchers to establish the initial knowledge state of students as well as to attempt to measure some of the impacts of innovative instructional interventions. Before now, few of the existing instruments were constructed upon a solid list of clearly articulated and widely agreed upon learning objectives. Moving beyond the 10-year old Astronomy Diagnostics Test, we have developed and validated a new assessment instrument that is tightly aligned to the consensus learning goals stated by the American Astronomical Society - Chair's Conference on ASTRO 101, the American Association of the Advancement of Science's Project 2061 Benchmarks, and the National Research Council's National Science Education Standards. Researchers from the Cognition in Astronomy, Physics and Earth sciences Research (CAPER) Team at the University of Wyoming's Science and Math Teaching Center (UWYO SMTC) designed a criterion-referenced assessment tool, called the Test Of Astronomy STandards (TOAST). Through iterative development, this multiple-choice instrument has a high degree of reliability and validity for instructors and researchers needing information on students’ initial knowledge state at the beginning of a course and can be used, in aggregate, to help measure the impact of course-length duration instructional strategies for undergraduate science survey courses with learning goals tightly aligned to the consensus goals of the astronomy education community.

Dynamic trunk stabilization: a conceptual back injury prevention program for volleyball athletes.

PubMed

Smith, Chad E; Nyland, John; Caudill, Paul; Brosky, Joseph; Caborn, David N M

2008-11-01

The sport of volleyball creates considerable dynamic trunk stability demands. Back injury occurs all too frequently in volleyball, particularly among female athletes. The purpose of this clinical commentary is to review functional anatomy, muscle coactivation strategies, assessment of trunk muscle performance, and the characteristics of effective exercises for the trunk or core. From this information, a conceptual progressive 3-phase volleyball-specific training program is presented to improve dynamic trunk stability and to potentially reduce the incidence of back injury among volleyball athletes. Phase 1 addresses low-velocity motor control, kinesthetic awareness, and endurance, with the clinician providing cues to teach achievement of biomechanically neutral spine alignment. Phase 2 focuses on progressively higher velocity dynamic multiplanar endurance, coordination, and strength-power challenges integrating upper and lower extremity movements, while maintaining neutral spine alignment. Phase 3 integrates volleyball-specific skill simulations by breaking down composite movement patterns into their component parts, with differing dynamic trunk stability requirements, while maintaining neutral spine alignment. Prospective research is needed to validate the efficacy of this program.

Development of Impact Assessment Methodologies for Environmental Sustainability

EPA Science Inventory

Sustainability has been discussed for many years, with no consensus on how to ensure that environmental sustainability is reached or even that progress is made in the right direction. The Brundtland Commission statement that sustainability “meets the needs of the present without...

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0

PubMed Central

Llorens, Carlos; Futami, Ricardo; Covelli, Laura; Domínguez-Escribá, Laura; Viu, Jose M.; Tamarit, Daniel; Aguilar-Rodríguez, Jose; Vicente-Ripolles, Miguel; Fuster, Gonzalo; Bernet, Guillermo P.; Maumus, Florian; Munoz-Pomer, Alfonso; Sempere, Jose M.; Latorre, Amparo; Moya, Andres

2011-01-01

This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants. Among other features, in terms of the aforementioned topics, this update adds: (i) a variety of descriptions and reviews distributed in multiple web pages; (ii) protein-based phylogenies, where phylogenetic levels are assigned to distinct classified elements; (iii) a collection of multiple alignments, lineage-specific hidden Markov models and consensus sequences, called GyDB collection; (iv) updated RefSeq databases and BLAST and HMM servers to facilitate sequence characterization of new LTR retroelement and caulimovirus queries; and (v) a bibliographic server. GyDB 2.0 is available at http://gydb.org. PMID:21036865

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0.

PubMed

Llorens, Carlos; Futami, Ricardo; Covelli, Laura; Domínguez-Escribá, Laura; Viu, Jose M; Tamarit, Daniel; Aguilar-Rodríguez, Jose; Vicente-Ripolles, Miguel; Fuster, Gonzalo; Bernet, Guillermo P; Maumus, Florian; Munoz-Pomer, Alfonso; Sempere, Jose M; Latorre, Amparo; Moya, Andres

2011-01-01

This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants. Among other features, in terms of the aforementioned topics, this update adds: (i) a variety of descriptions and reviews distributed in multiple web pages; (ii) protein-based phylogenies, where phylogenetic levels are assigned to distinct classified elements; (iii) a collection of multiple alignments, lineage-specific hidden Markov models and consensus sequences, called GyDB collection; (iv) updated RefSeq databases and BLAST and HMM servers to facilitate sequence characterization of new LTR retroelement and caulimovirus queries; and (v) a bibliographic server. GyDB 2.0 is available at http://gydb.org.

A common monitoring framework for ending preventable maternal mortality, 2015-2030: phase I of a multi-step process.

PubMed

Moran, Allisyn C; Jolivet, R Rima; Chou, Doris; Dalglish, Sarah L; Hill, Kathleen; Ramsey, Kate; Rawlins, Barbara; Say, Lale

2016-08-26

While global maternal mortality declined 44 % between 1990 and 2015, the majority of countries fell short of attaining Millennium Development Goal targets. The Sustainable Development Goals (SDGs), adopted in late 2015, include a target to reduce national maternal mortality ratios (MMR) to achieve a global average of 70 per 100,000 live births by 2030. A comprehensive paper outlining Strategies toward Ending Preventable Maternal Mortality (EPMM) was launched in February 2015 to support achievement of the SDG global targets. To date, there has not been consensus on a set of core metrics to track progress toward the overall global maternal mortality target, which has made it difficult to systematically monitor maternal health status and programs over time. The World Health Organization (WHO), Maternal Health Taskforce (MHTF), and the US Agency for International Development (USAID) along with its flagship Maternal and Child Survival Program (MCSP), facilitated a consultative process to seek consensus on maternal health indicators for global monitoring and reporting by all countries. Consensus was reached on 12 indicators and four priority areas for further indicator development and testing. These indicators are being harmonized with the Every Newborn Action Plan core metrics for a joint global maternal newborn monitoring framework. Next steps include a similar process to agree upon indicators to monitor social, political and economic determinants of maternal health and survival highlighted in the EPMM strategies. This process provides a foundation for the maternal health community to work collaboratively to track progress on core global indicators. It is important that actors continue to work together through transparent and participatory processes to track progress to end preventable maternal mortality and achieve the SDG maternal mortality targets.

A consensus approach to improving patient adherence and persistence with topical treatment for actinic keratosis

PubMed Central

Stockfleth, Eggert; Peris, Ketty; Guillen, Carlos; Cerio, Rino; Basset-Seguin, Nicole; Foley, Peter; Sanches, José; Culshaw, Alex; Erntoft, Sandra; Lebwohl, Mark

2015-01-01

Background Topical therapy is important in the treatment of actinic keratosis, but guidance for improving adherence/persistence during topical therapy is still lacking. Objectives To utilize expert consensus to generate a list of recommendations to improve real-world efficacy when prescribing topical therapy for actinic keratosis. Methods An expert panel of eight dermatologists was convened to generate recommendations based on facilitated discussion and consensus generation using a modified Delphi session. The recommendations were ratified with the expert panel. Results Facilitated discussion generated 31 issues within five themes, which were prioritized using expert voting. Consensus was achieved on the importance of short and simple treatment regimens for maximizing patient compliance, physician awareness of the progression of actinic keratosis to squamous cell carcinoma, provision of appropriate patient information, and the use of effective communication strategies to educate physicians about actinic keratosis. Based on these key findings, eight recommendations were generated. Conclusions The recommendations will assist physicians when prescribing topical actinic keratosis therapy. Further research should focus on the types of patient outcomes that are influenced by the characteristics of topical field therapy. PMID:25865875

Modeling of the coupled magnetospheric and neutral wind dynamos

NASA Technical Reports Server (NTRS)

Thayer, Jeffrey P.

1994-01-01

This report summarizes the progress made in the first year of NASA Grant No. NAGW-3508 entitled 'Modeling of the Coupled Magnetospheric and Neutral Wind Dynamos.' The approach taken has been to impose magnetospheric boundary conditions with either pure voltage or current characteristics and solve the neutral wind dynamo equation under these conditions. The imposed boundary conditions determine whether the neutral wind dynamo will contribute to the high-latitude current system or the electric potential. The semi-annual technical report, dated December 15, 1993, provides further detail describing the scientific and numerical approach of the project. The numerical development has progressed and the dynamo solution for the case when the magnetosphere acts as a voltage source has been evaluated completely using spectral techniques. The simulation provides the field-aligned current distribution at high latitudes due to the neutral wind dynamo. A number of geophysical conditions can be simulated to evaluate the importance of the neutral wind dynamo contribution to the field-aligned current system. On average, field-aligned currents generated by the neutral wind dynamo contributed as much as 30 percent to the large-scale field-aligned current system driven by the magnetosphere. A term analysis of the high-latitude neutral wind dynamo equation describing the field aligned current distribution has also been developed to illustrate the important contributing factors involved in the process. The case describing the neutral dynamo response for a magnetosphere acting as a pure current generator requires the existing spectral code to be extended to a pseudo-spectral method and is currently under development.

Fourier transform power spectrum is a potential measure of tissue alignment in standard MRI: A multiple sclerosis study.

PubMed

Sharma, Shrushrita; Zhang, Yunyan

2017-01-01

Loss of tissue coherency in brain white matter is found in many neurological diseases such as multiple sclerosis (MS). While several approaches have been proposed to evaluate white matter coherency including fractional anisotropy and fiber tracking in diffusion-weighted imaging, few are available for standard magnetic resonance imaging (MRI). Here we present an image post-processing method for this purpose based on Fourier transform (FT) power spectrum. T2-weighted images were collected from 19 patients (10 relapsing-remitting and 9 secondary progressive MS) and 19 age- and gender-matched controls. Image processing steps included: computation, normalization, and thresholding of FT power spectrum; determination of tissue alignment profile and dominant alignment direction; and calculation of alignment complexity using a new measure named angular entropy. To test the validity of this method, we used a highly organized brain white matter structure, corpus callosum. Six regions of interest were examined from the left, central and right aspects of both genu and splenium. We found that the dominant orientation of each ROI derived from our method was significantly correlated with the predicted directions based on anatomy. There was greater angular entropy in patients than controls, and a trend to be greater in secondary progressive MS patients. These findings suggest that it is possible to detect tissue alignment and anisotropy using traditional MRI, which are routinely acquired in clinical practice. Analysis of FT power spectrum may become a new approach for advancing the evaluation and management of patients with MS and similar disorders. Further confirmation is warranted.

Static knee alignment and its association with radiographic knee osteoarthritis.

PubMed

Teichtahl, A J; Cicuttini, F M; Janakiramanan, N; Davis, S R; Wluka, A E

2006-09-01

Although knee alignment is associated with the progression of knee osteoarthritis (OA), it is unclear which features that characterize radiographic OA are related to alignment. The aim of this study was to examine the relationship between static knee joint alignment (measured as a continuous variable) and the radiographic features of knee OA (joint space narrowing and osteophytes). One hundred and twenty one adults with symptomatic knee OA were recruited using a combined strategy including referral from specialist centres, arthritis support groups and media advertising. X-rays were performed to classify the severity of disease and to determine static knee alignment. Increasing varus knee alignment was associated with increasing risk of medial compartment joint space narrowing (P < 0.001) and osteophytes (P = 0.005). Increasing valgus knee alignment was associated with an increased risk for lateral compartment joint space narrowing (P < 0.001) and osteophytes (P = 0.002). This study has demonstrated that the static knee angle, measured as a continuous variable, is an important determinant of the compartment-specific features of radiographic knee OA. Further work is required to determine whether interventions aimed at correcting these relatively minor levels of varus and valgus angulation will have an effect on the risk of tibiofemoral OA.

Does Tibial Slope Affect Perception of Coronal Alignment on a Standing Anteroposterior Radiograph?

PubMed

Schwartz, Adam J; Ravi, Bheeshma; Kransdorf, Mark J; Clarke, Henry D

2017-07-01

A standing anteroposterior (AP) radiograph is commonly used to evaluate coronal alignment following total knee arthroplasty (TKA). The impact of coronal alignment on TKA outcomes is controversial, perhaps due to variability in imaging and/or measurement technique. We sought to quantify the effect of image rotation and tibial slope on coronal alignment. Using a standard extramedullary tibial alignment guide, 3 cadaver legs were cut to accept a tibial tray at 0°, 3°, and 7° of slope. A computed tomography scan of the entire tibia was obtained for each specimen to confirm neutral coronal alignment. Images were then obtained at progressive 10° intervals of internal and external rotation up to 40° maximum in each direction. Images were then randomized and 5 blinded TKA surgeons were asked to determine coronal alignment. Continuous data values were transformed to categorical data (neutral [0], valgus [L], and varus [R]). Each 10° interval of external rotation of a 7° sloped tibial cut (or relative internal rotation of a tibial component viewed in the AP plane) resulted in perception of an additional 0.75° of varus. The slope of the proximal tibia bone cut should be taken into account when measuring coronal alignment on a standing AP radiograph. Copyright © 2017 Elsevier Inc. All rights reserved.

Accelerated probabilistic inference of RNA structure evolution

PubMed Central

Holmes, Ian

2005-01-01

Background Pairwise stochastic context-free grammars (Pair SCFGs) are powerful tools for evolutionary analysis of RNA, including simultaneous RNA sequence alignment and secondary structure prediction, but the associated algorithms are intensive in both CPU and memory usage. The same problem is faced by other RNA alignment-and-folding algorithms based on Sankoff's 1985 algorithm. It is therefore desirable to constrain such algorithms, by pre-processing the sequences and using this first pass to limit the range of structures and/or alignments that can be considered. Results We demonstrate how flexible classes of constraint can be imposed, greatly reducing the computational costs while maintaining a high quality of structural homology prediction. Any score-attributed context-free grammar (e.g. energy-based scoring schemes, or conditionally normalized Pair SCFGs) is amenable to this treatment. It is now possible to combine independent structural and alignment constraints of unprecedented general flexibility in Pair SCFG alignment algorithms. We outline several applications to the bioinformatics of RNA sequence and structure, including Waterman-Eggert N-best alignments and progressive multiple alignment. We evaluate the performance of the algorithm on test examples from the RFAM database. Conclusion A program, Stemloc, that implements these algorithms for efficient RNA sequence alignment and structure prediction is available under the GNU General Public License. PMID:15790387

Alignment-independent technique for 3D QSAR analysis

NASA Astrophysics Data System (ADS)

Wilkes, Jon G.; Stoyanova-Slavova, Iva B.; Buzatu, Dan A.

2016-04-01

Molecular biochemistry is controlled by 3D phenomena but structure-activity models based on 3D descriptors are infrequently used for large data sets because of the computational overhead for determining molecular conformations. A diverse dataset of 146 androgen receptor binders was used to investigate how different methods for defining molecular conformations affect the performance of 3D-quantitative spectral data activity relationship models. Molecular conformations tested: (1) global minimum of molecules' potential energy surface; (2) alignment-to-templates using equal electronic and steric force field contributions; (3) alignment using contributions "Best-for-Each" template; (4) non-energy optimized, non-aligned (2D > 3D). Aggregate predictions from models were compared. Highest average coefficients of determination ranged from R Test 2 = 0.56 to 0.61. The best model using 2D > 3D (imported directly from ChemSpider) produced R Test 2 = 0.61. It was superior to energy-minimized and conformation-aligned models and was achieved in only 3-7 % of the time required using the other conformation strategies. Predictions averaged from models built on different conformations achieved a consensus R Test 2 = 0.65. The best 2D > 3D model was analyzed for underlying structure-activity relationships. For the compound strongest binding to the androgen receptor, 10 substructural features contributing to binding were flagged. Utility of 2D > 3D was compared for two other activity endpoints, each modeling a medium sized data set. Results suggested that large scale, accurate predictions using 2D > 3D SDAR descriptors may be produced for interactions involving endocrine system nuclear receptors and other data sets in which strongest activities are produced by fairly inflexible substrates.

iCivics

ERIC Educational Resources Information Center

Wormeli, Rick

2012-01-01

According to former Supreme Court Judge Sandra Day O'Connor, active citizenship requires that students know how to persuade others by logic, seek consensus, understand and create constructive dissent, and practice other vital critical-thinking skills. However, in the 2010 National Assessment of Educational Progress in civics, only one in four…

Culture: The missing link in health research.

PubMed

Kagawa Singer, M; Dressler, W; George, S

2016-12-01

Culture is essential for humans to exist. Yet surprisingly little attention has been paid to identifying how culture works or developing standards to guide the application of this concept in health research. This paper describes a multidisciplinary effort to find consensus on essential elements of a definition of culture to guide researchers in studying how cultural processes influence health and health behaviors. We first highlight the lack of progress made in the health sciences to explain differences between population groups, and then identify 10 key barriers in research impeding progress in more effectively and rapidly realizing equity in health outcomes. Second, we highlight the primarily mono-cultural lens through which health behavior is currently conceptualized, third, we present a consensus definition of culture as an integrating framework, and last, we provide guidelines to more effectively operationalize the concept of culture for health research. We hope this effort will be useful to researchers, reviewers, and funders alike. Copyright © 2016 Elsevier Ltd. All rights reserved.

Exploring Alignment among Learning Progressions, Teacher-Designed Formative Assessment Tasks, and Student Growth: Results of a Four-Year Study

ERIC Educational Resources Information Center

Furtak, Erin Marie; Circi, Ruhan; Heredia, Sara C.

2018-01-01

This article describes a 4-year study of experienced high school biology teachers' participation in a five-step professional development experience in which they iteratively studied student ideas with the support of a set of learning progressions, designed formative assessment activities, practiced using those activities with their students,…

Ethics in American Health 2: An Ethical Framework for Health System Reform

PubMed Central

2008-01-01

I argue that an ethical vision resting on explicitly articulated values and norms is critical to ensuring comprehensive health reform. Reform requires a consensus on the public good transcending self-interest and narrow agendas and underpinning collective action for universal coverage. In what I call shared health governance, individuals, providers, and institutions all have essential roles in achieving health goals and work together to create a positive environment for health. This ethical paradigm provides (1) reasoned consensus through a joint scientific and deliberative approach to judge the value of a health care intervention; (2) a method for achieving consensus that differs from aggregate tools such as a strict majority vote; (3) combined technical and ethical rationality for collective choice; (4) a joint clinical and economic approach combining efficiency with equity, but with economic solutions following and complementing clinical progress; and (5) protection for disabled individuals from discrimination. PMID:18703448

Ethics in American health 2: an ethical framework for health system reform.

PubMed

Ruger, Jennifer Prah

2008-10-01

I argue that an ethical vision resting on explicitly articulated values and norms is critical to ensuring comprehensive health reform. Reform requires a consensus on the public good transcending self-interest and narrow agendas and underpinning collective action for universal coverage. In what I call shared health governance, individuals, providers, and institutions all have essential roles in achieving health goals and work together to create a positive environment for health. This ethical paradigm provides (1) reasoned consensus through a joint scientific and deliberative approach to judge the value of a health care intervention; (2) a method for achieving consensus that differs from aggregate tools such as a strict majority vote; (3) combined technical and ethical rationality for collective choice; (4) a joint clinical and economic approach combining efficiency with equity, but with economic solutions following and complementing clinical progress; and (5) protection for disabled individuals from discrimination.

Closing the Expectations Gap 2013. 50-State Progress Report on the Alignment of State K-12 Policies and Practice with the Demands of College and Careers

ERIC Educational Resources Information Center

Achieve, Inc., 2013

2013-01-01

This eighth annual report has taken a directional change from prior years where the primary aim was preparing students to graduate from high school. The new focus is on the K-12 alignment where, at the direction of 48 states, the National Governors Association, and the Council of Chief State School Officers, the Common Core State Standards were…

Surrogate endpoints for clinical trials in primary sclerosing cholangitis: Review and results from an International PSC Study Group consensus process.

PubMed

Ponsioen, Cyriel Y; Chapman, Roger W; Chazouillères, Olivier; Hirschfield, Gideon M; Karlsen, Tom H; Lohse, Ansgar W; Pinzani, Massimo; Schrumpf, Erik; Trauner, Michael; Gores, Gregory J

2016-04-01

Primary sclerosing cholangitis (PSC) is a rare, but serious, cholestatic disease for which, to date, no effective therapy exists to halt disease progression toward end-stage liver disease. Clinical trial design to study drugs that improve prognosis is hampered by the relatively low event rate of clinically relevant endpoints. To overcome this shortcoming, there is an urgent need to identify appropriate surrogate endpoints. At present, there are no established surrogate endpoints. This article provides a critical review and describes the results of a consensus process initiated by the International PSC Study Group to delineate appropriate candidate surrogate endpoints at present for clinical trials in this frequently dismal disease. The consensus process resulted in a shortlist of five candidates as surrogate endpoints for measuring disease progression: alkaline phosphatase (ALP); transient elastography (TE); histology; combination of ALP+histology; and bilirubin. Of these, histology, ALP, and TE came out as the most promising. However, the expert panel concluded that no biomarker currently exceeds level 3 validation. Combining multiple endpoints is advisable. At present, there are insufficient data to support level 2 validation for any surrogate endpoint in PSC. Concerted efforts by all stakeholders are highly needed. Novel, promising noninvasive biomarkers are under study and should be incorporated as exploratory endpoints in clinical trials. © 2015 by the American Association for the Study of Liver Diseases.

Policy and Technology Readiness: Engaging the User and Developer Community to Develop a Research Roadmap

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

Olson, Jarrod; Barr, Jonathan L.; Burtner, Edwin R.

A key challenge for research roadmapping in the crisis response and management domain is articulation of a shared vision that describes what the future can and should include. Visioning allows for far-reaching stakeholder engagement that can properly align research with stakeholders needs. Engagement includes feedback from researchers, policy makers, general public, and end-users on technical and non-technical factors. This work articulates a process and framework for the construction and maintenance of a stakeholder-centric research vision and roadmap in the emergency management domain. This novel roadmapping process integrates three pieces: analysis of the research and technology landscape, visioning, and stakeholder engagement.more » Our structured engagement process elicits research foci for the roadmap based on relevance to stakeholder mission, identifies collaborators, and builds consensus around the roadmap priorities. We find that the vision process and vision storyboard helps SMEs conceptualize and discuss a technology's strengths, weaknesses, and alignment with needs« less

A research agenda for bridging the 'quality chasm.'.

PubMed

Fernandopulle, Rushika; Ferris, Timothy; Epstein, Arnold; McNeil, Barbara; Newhouse, Joseph; Pisano, Gary; Blumenthal, David

2003-01-01

Realizing the vision of the IOM's landmark report, Crossing the Quality Chasm, will require new knowledge to support new policy and management. This paper lays out a research agenda that must be pursued if the health care system is to bridge the quality chasm. Based on a consensus process involving leading health care researchers and authorities, the paper highlights knowledge gaps and research directions in five areas identified by the Quality Chasm report as critical to its goals of building organizational supports for change; applying evidence to health care delivery; developing information technology; aligning payment policies with quality improvement; and preparing the workforce.

A laid-back trip through the Hennigian Forests

PubMed Central

2017-01-01

Background This paper is a comment on the idea of matrix-free Cladistics. Demonstration of this idea’s efficiency is a major goal of the study. Within the proposed framework, the ordinary (phenetic) matrix is necessary only as “source” of Hennigian trees, not as a primary subject of the analysis. Switching from the matrix-based thinking to the matrix-free Cladistic approach clearly reveals that optimizations of the character-state changes are related not to the real processes, but to the form of the data representation. Methods We focused our study on the binary data. We wrote the simple ruby-based script FORESTER version 1.0 that helps represent a binary matrix as an array of the rooted trees (as a “Hennigian forest”). The binary representations of the genomic (DNA) data have been made by script 1001. The Average Consensus method as well as the standard Maximum Parsimony (MP) approach has been used to analyze the data. Principle findings The binary matrix may be easily re-written as a set of rooted trees (maximal relationships). The latter might be analyzed by the Average Consensus method. Paradoxically, this method, if applied to the Hennigian forests, in principle can help to identify clades despite the absence of the direct evidence from the primary data. Our approach may handle the clock- or non clock-like matrices, as well as the hypothetical, molecular or morphological data. Discussion Our proposal clearly differs from the numerous phenetic alignment-free techniques of the construction of the phylogenetic trees. Dealing with the relations, not with the actual “data” also distinguishes our approach from all optimization-based methods, if the optimization is defined as a way to reconstruct the sequences of the character-state changes on a tree, either the standard alignment-based techniques or the “direct” alignment-free procedure. We are not viewing our recent framework as an alternative to the three-taxon statement analysis (3TA), but there are two major differences between our recent proposal and the 3TA, as originally designed and implemented: (1) the 3TA deals with the three-taxon statements or minimal relationships. According to the logic of 3TA, the set of the minimal trees must be established as a binary matrix and used as an input for the parsimony program. In this paper, we operate directly with maximal relationships written just as trees, not as binary matrices, while also using the Average Consensus method instead of the MP analysis. The solely ‘reversal’-based groups can always be found by our method without the separate scoring of the putative reversals before analyses. PMID:28740753

Dinucleotide controlled null models for comparative RNA gene prediction.

PubMed

Gesell, Tanja; Washietl, Stefan

2008-05-27

Comparative prediction of RNA structures can be used to identify functional noncoding RNAs in genomic screens. It was shown recently by Babak et al. [BMC Bioinformatics. 8:33] that RNA gene prediction programs can be biased by the genomic dinucleotide content, in particular those programs using a thermodynamic folding model including stacking energies. As a consequence, there is need for dinucleotide-preserving control strategies to assess the significance of such predictions. While there have been randomization algorithms for single sequences for many years, the problem has remained challenging for multiple alignments and there is currently no algorithm available. We present a program called SISSIz that simulates multiple alignments of a given average dinucleotide content. Meeting additional requirements of an accurate null model, the randomized alignments are on average of the same sequence diversity and preserve local conservation and gap patterns. We make use of a phylogenetic substitution model that includes overlapping dependencies and site-specific rates. Using fast heuristics and a distance based approach, a tree is estimated under this model which is used to guide the simulations. The new algorithm is tested on vertebrate genomic alignments and the effect on RNA structure predictions is studied. In addition, we directly combined the new null model with the RNAalifold consensus folding algorithm giving a new variant of a thermodynamic structure based RNA gene finding program that is not biased by the dinucleotide content. SISSIz implements an efficient algorithm to randomize multiple alignments preserving dinucleotide content. It can be used to get more accurate estimates of false positive rates of existing programs, to produce negative controls for the training of machine learning based programs, or as standalone RNA gene finding program. Other applications in comparative genomics that require randomization of multiple alignments can be considered. SISSIz is available as open source C code that can be compiled for every major platform and downloaded here: http://sourceforge.net/projects/sissiz.

Precancerous Skin Lesions.

PubMed

Ferrándiz, C; Malvehy, J; Guillén, C; Ferrándiz-Pulido, C; Fernández-Figueras, M

Certain clinically and histologically recognizable skin lesions with a degree of risk of progression to squamous cell carcinoma have been traditionally grouped as precancerous skin conditions but now tend to be classified as in situ carcinomas. This consensus statement discusses various aspects of these lesions: their evaluation by means of clinical and histopathologic features, the initial evaluation of the patient, the identification of risk factors for progression, and the diagnostic and treatment strategies available today. Copyright © 2016 AEDV. Publicado por Elsevier España, S.L.U. All rights reserved.

An independent jury-based consensus conference model for the development of recommendations in medico-surgical practice.

PubMed

Lesurtel, Mickaël; Perrier, Arnaud; Bossuyt, Patrick M M; Langer, Bernard; Clavien, Pierre-Alain

2014-03-01

There is an increasing demand for standardization in the choice of treatments for specific conditions, so-called personalized medicine. The task is far from trivial, because the perspectives from many stakeholders must be respected, including patients and health care providers, as well as payers or governments to better control costs while optimizing quality of care. One approach to provide widely accepted therapies is the consensus conference. We describe a novel methodology to achieve consensus in controversial areas with the main goal to minimize biases. The principle of this approach relies on a clear distinction between those who provide the evidence (experts) and those who draw the final recommendations (the jury). The jury consists of individuals with sufficient background knowledge to cover the perspectives of all stakeholders' without being involved directly in the topic under evaluation. The organizing committee, the experts, and the jury interact within 3 phases: Preparation, the actual consensus conference, and deliberations. Each question is addressed by a panel of experts, leading to the proposition of recommendations at the conference meeting, which are challenged by the jury and the audience. Based on all available information, the jury finalizes the consensus recommendations, which are eventually published and made available to all. This novel model of consensus conference allows the construction of consensual, evidence-based, explicit recommendations for therapies in a process that may also identify issues for further research, eventually fostering progress in the field. Copyright © 2014 Mosby, Inc. All rights reserved.

Importance of orthotic subtalar alignment for development and gait of children with cerebral palsy.

PubMed

Carmick, Judy

2012-01-01

This case report addresses the assumption that ankle and foot orthoses assist children with cerebral palsy. Outcome research reports are not consistent. Clinical observations and research studies suggest that inappropriate fit and design of orthoses may contribute to poor outcomes. In particular, problems occur when the subtalar joint is out of alignment as children often compensate with unwanted movement patterns that affect progress, development, and function. Four cases are presented to demonstrate problems that can occur when ankle-foot or supramalleolar orthoses are not cast in subtalar neutral. Physical therapists can use their clinical observation skills to evaluate the proper fit and alignment of orthoses for children with cerebral palsy.

Seismic evidence for flow in the hydrated mantle wedge of the Ryukyu subduction zone

PubMed Central

Nagaya, Takayoshi; Walker, Andrew M.; Wookey, James; Wallis, Simon R.; Ishii, Kazuhiko; Kendall, J. -Michael

2016-01-01

It is widely accepted that water-rich serpentinite domains are commonly present in the mantle above shallow subducting slabs and play key roles in controlling the geochemical cycling and physical properties of subduction zones. Thermal and petrological models show the dominant serpentine mineral is antigorite. However, there is no good consensus on the amount, distribution and alignment of this mineral. Seismic velocities are commonly used to identify antigorite-rich domains, but antigorite is highly-anisotropic and depending on the seismic ray path, its properties can be very difficult to distinguish from non-hydrated olivine-rich mantle. Here, we utilize this anisotropy and show how an analysis of seismic anisotropy that incorporates measured ray path geometries in the Ryukyu arc can constrain the distribution, orientation and amount of antigorite. We find more than 54% of the wedge must consist of antigorite and the alignment must change from vertically aligned to parallel to the slab. This orientation change suggests convective flow in the hydrated forearc mantle. Shear wave splitting analysis in other subduction zones indicates large-scale serpentinization and forearc mantle convection are likely to be more widespread than generally recognized. The view that the forearc mantle of cold subduction zones is dry needs to be reassessed. PMID:27436676

Seismic evidence for flow in the hydrated mantle wedge of the Ryukyu subduction zone.

PubMed

Nagaya, Takayoshi; Walker, Andrew M; Wookey, James; Wallis, Simon R; Ishii, Kazuhiko; Kendall, J-Michael

2016-07-20

It is widely accepted that water-rich serpentinite domains are commonly present in the mantle above shallow subducting slabs and play key roles in controlling the geochemical cycling and physical properties of subduction zones. Thermal and petrological models show the dominant serpentine mineral is antigorite. However, there is no good consensus on the amount, distribution and alignment of this mineral. Seismic velocities are commonly used to identify antigorite-rich domains, but antigorite is highly-anisotropic and depending on the seismic ray path, its properties can be very difficult to distinguish from non-hydrated olivine-rich mantle. Here, we utilize this anisotropy and show how an analysis of seismic anisotropy that incorporates measured ray path geometries in the Ryukyu arc can constrain the distribution, orientation and amount of antigorite. We find more than 54% of the wedge must consist of antigorite and the alignment must change from vertically aligned to parallel to the slab. This orientation change suggests convective flow in the hydrated forearc mantle. Shear wave splitting analysis in other subduction zones indicates large-scale serpentinization and forearc mantle convection are likely to be more widespread than generally recognized. The view that the forearc mantle of cold subduction zones is dry needs to be reassessed.

Genetic dissection of the consensus sequence for the class 2 and class 3 flagellar promoters

PubMed Central

Wozniak, Christopher E.; Hughes, Kelly T.

2008-01-01

Summary Computational searches for DNA binding sites often utilize consensus sequences. These search models make assumptions that the frequency of a base pair in an alignment relates to the base pair’s importance in binding and presume that base pairs contribute independently to the overall interaction with the DNA binding protein. These two assumptions have generally been found to be accurate for DNA binding sites. However, these assumptions are often not satisfied for promoters, which are involved in additional steps in transcription initiation after RNA polymerase has bound to the DNA. To test these assumptions for the flagellar regulatory hierarchy, class 2 and class 3 flagellar promoters were randomly mutagenized in Salmonella. Important positions were then saturated for mutagenesis and compared to scores calculated from the consensus sequence. Double mutants were constructed to determine how mutations combined for each promoter type. Mutations in the binding site for FlhD4C2, the activator of class 2 promoters, better satisfied the assumptions for the binding model than did mutations in the class 3 promoter, which is recognized by the σ28 transcription factor. These in vivo results indicate that the activator sites within flagellar promoters can be modeled using simple assumptions but that the DNA sequences recognized by the flagellar sigma factor require more complex models. PMID:18486950

Consensus-based Recommendations for Research Priorities Related to Interventions to Safeguard Patient Safety in the Crowded Emergency Department

PubMed Central

Fee, Christopher; Hall, Kendall; Morrison, J. Bradley; Stephens, Robert; Cosby, Karen; Fairbanks, Rollin (Terry) J.; Youngberg, Barbara; Lenehan, Gail; Abualenain, Jameel; O’Connor, Kevin; Wears, Robert

2012-01-01

This article describes the results of the Interventions to Safeguard Safety breakout session of the 2011 Academic Emergency Medicine (AEM) consensus conference entitled “Interventions to Assure Quality in the Crowded Emergency Department.” Using a multistep nominal group technique, experts in emergency department (ED) crowding, patient safety, and systems engineering defined knowledge gaps and priority research questions related to the maintenance of safety in the crowded ED. Consensus was reached for seven research priorities related to interventions to maintain safety in the setting of a crowded ED. Included among these are: 1) How do routine corrective processes and compensating mechanism change during crowding? 2) What metrics should be used to determine ED safety? 3) How can checklists ensure safer care and what factors contribute to their success or failure? 4) What constitutes safe staffing levels / ratios? 5) How can we align emergency medicine (EM)-specific patient safety issues with national patient safety issues? 6) How can we develop metrics and skills to recognize when an ED is getting close to catastrophic overload conditions? and 7) What can EM learn from experts and modeling from fields outside of medicine to develop innovative solutions? These priorities have the potential to inform future clinical and human factors research and extramural funding decisions related to this important topic. PMID:22168192

Advanced evolutionary molecular engineering to produce thermostable cellulase by using a small but efficient library.

PubMed

Ito, Y; Ikeuchi, A; Imamura, C

2013-01-01

We aimed at constructing thermostable cellulase variants of cellobiohydrolase II, derived from the mesophilic fungus Phanerochaete chrysosporium, by using an advanced evolutionary molecular engineering method. By aligning the amino acid sequences of the catalytic domains of five thermophilic fungal CBH2 and PcCBH2 proteins, we identified 45 positions where the PcCBH2 genes differ from the consensus sequence of two to five thermophilic fungal CBH2s. PcCBH2 variants with the consensus mutations were obtained by a cell-free translation system that was chosen for easy evaluation of thermostability. From the small library of consensus mutations, advantageous mutations for improving thermostability were found to occur with much higher frequency relative to a random library. To further improve thermostability, advantageous mutations were accumulated within the wild-type gene. Finally, we obtained the most thermostable variant Mall4, which contained all 15 advantageous mutations found in this study. This variant had the same specific cellulase activity as the wild type and retained sufficient activity at 50°C for >72 h, whereas wild-type PcCBH2 retained much less activity under the same conditions. The history of the accumulation process indicated that evolution of PcCBH2 toward improved thermostability was ideally and rapidly accomplished through the evolutionary process employed in this study.

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

PubMed Central

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

2016-01-01

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

Generic accelerated sequence alignment in SeqAn using vectorization and multi-threading.

PubMed

Rahn, René; Budach, Stefan; Costanza, Pascal; Ehrhardt, Marcel; Hancox, Jonny; Reinert, Knut

2018-05-03

Pairwise sequence alignment is undoubtedly a central tool in many bioinformatics analyses. In this paper, we present a generically accelerated module for pairwise sequence alignments applicable for a broad range of applications. In our module, we unified the standard dynamic programming kernel used for pairwise sequence alignments and extended it with a generalized inter-sequence vectorization layout, such that many alignments can be computed simultaneously by exploiting SIMD (Single Instruction Multiple Data) instructions of modern processors. We then extended the module by adding two layers of thread-level parallelization, where we a) distribute many independent alignments on multiple threads and b) inherently parallelize a single alignment computation using a work stealing approach producing a dynamic wavefront progressing along the minor diagonal. We evaluated our alignment vectorization and parallelization on different processors, including the newest Intel® Xeon® (Skylake) and Intel® Xeon Phi™ (KNL) processors, and use cases. The instruction set AVX512-BW (Byte and Word), available on Skylake processors, can genuinely improve the performance of vectorized alignments. We could run single alignments 1600 times faster on the Xeon Phi™ and 1400 times faster on the Xeon® than executing them with our previous sequential alignment module. The module is programmed in C++ using the SeqAn (Reinert et al., 2017) library and distributed with version 2.4. under the BSD license. We support SSE4, AVX2, AVX512 instructions and included UME::SIMD, a SIMD-instruction wrapper library, to extend our module for further instruction sets. We thoroughly test all alignment components with all major C++ compilers on various platforms. rene.rahn@fu-berlin.de.

Utilization and Harmonization of Adult Accelerometry Data: Review and Expert Consensus.

PubMed

Wijndaele, Katrien; Westgate, Kate; Stephens, Samantha K; Blair, Steven N; Bull, Fiona C; Chastin, Sebastien F M; Dunstan, David W; Ekelund, Ulf; Esliger, Dale W; Freedson, Patty S; Granat, Malcolm H; Matthews, Charles E; Owen, Neville; Rowlands, Alex V; Sherar, Lauren B; Tremblay, Mark S; Troiano, Richard P; Brage, Søren; Healy, Genevieve N

2015-10-01

This study aimed to describe the scope of accelerometry data collected internationally in adults and to obtain a consensus from measurement experts regarding the optimal strategies to harmonize international accelerometry data. In March 2014, a comprehensive review was undertaken to identify studies that collected accelerometry data in adults (sample size, n ≥ 400). In addition, 20 physical activity experts were invited to participate in a two-phase Delphi process to obtain consensus on the following: unique research opportunities available with such data, additional data required to address these opportunities, strategies for enabling comparisons between studies/countries, requirements for implementing/progressing such strategies, and value of a global repository of accelerometry data. The review identified accelerometry data from more than 275,000 adults from 76 studies across 36 countries. Consensus was achieved after two rounds of the Delphi process; 18 experts participated in one or both rounds. The key opportunities highlighted were the ability for cross-country/cross-population comparisons and the analytic options available with the larger heterogeneity and greater statistical power. Basic sociodemographic and anthropometric data were considered a prerequisite for this. Disclosure of monitor specifications and protocols for data collection and processing were deemed essential to enable comparison and data harmonization. There was strong consensus that standardization of data collection, processing, and analytical procedures was needed. To implement these strategies, communication and consensus among researchers, development of an online infrastructure, and methodological comparison work were required. There was consensus that a global accelerometry data repository would be beneficial and worthwhile. This foundational resource can lead to implementation of key priority areas and identification of future directions in physical activity epidemiology, population monitoring, and burden of disease estimates.

Degradation of cognitive timing mechanisms in behavioural variant frontotemporal dementia

PubMed Central

Henley, Susie M.D.; Downey, Laura E.; Nicholas, Jennifer M.; Kinnunen, Kirsi M.; Golden, Hannah L.; Buckley, Aisling; Mahoney, Colin J.; Crutch, Sebastian J.

2014-01-01

The current study examined motor timing in frontotemporal dementia (FTD), which manifests as progressive deterioration in social, behavioural and cognitive functions. Twenty-patients fulfilling consensus clinical criteria for behavioural variant FTD (bvFTD), 11 patients fulfilling consensus clinical criteria for semantic-variant primary progressive aphasia (svPPA), four patients fulfilling criteria for nonfluent/agrammatic primary progressive aphasia (naPPA), eight patients fulfilling criteria for Alzheimer׳s disease (AD), and 31 controls were assessed on both an externally- and self-paced finger-tapping task requiring maintenance of a regular, 1500 ms beat over 50 taps. Grey and white matter correlates of deficits in motor timing were examined using voxel-based morphometry (VBM) and diffusion tensor imaging (DTI). bvFTD patients exhibited significant deficits in aspects of both externally- and self-paced tapping. Increased mean inter-response interval (faster than target tap time) in the self-paced task was associated with reduced grey matter volume in the cerebellum bilaterally, right middle temporal gyrus, and with increased axial diffusivity in the right superior longitudinal fasciculus, regions and tracts which have been suggested to be involved in a subcortical–cortical network of structures underlying timing abilities. This suggests that such structures can be affected in bvFTD, and that impaired motor timing may underlie some characteristics of the bvFTD phenotype. PMID:25447066

Neuropathological aspects of conservative treatment of scoliosis. A theoretical view point.

PubMed

Czupryna, Krzysztof; Nowotny-Czupryna, Olga; Nowotny, Janusz

2012-01-01

An upright body posture cannot be maintained passively for reasons including a high location of the centre of gravity (COG) and a small support area. Proper alignment of body parts is maintained automatically, tending towards a pattern encoded in the CNS. A particularly important role in posture regulation is played by the short muscles of the back, which respond to being stretched with a contraction. During the early phase of scoliosis, the CNS automatically corrects abnormalities, but over time habituation occurs and the CNS treats them as something normal. Any attempt to restore proper body alignment is treated as an error and CNS automatically restores this abnormal pattern. With a prolonged deviation in body part alignment, CNS treats it as a defect and runs compensatory mechanisms to restore the balance of the body as a whole. Balance is ensured by postural compensation, but this does not restore proper body part alignment. In the treatment of scoliosis, it is important both to slow down progression and to prevent the development of abnormal postural habits, which are part of a vicious circle even without progression. Secondary prevention is therefore needed in all patients. Passive observation limits the possibilities for prevention and contradicts the principle of early implementation of rehabilitation. Depending on the size of the angle of curvature, recommended treatments of scoliosis comprise observation, corset bracing, and surgery. Physiotherapy is often treated as an unconventional and ineffective treatment. Often, the biggest problem is transferring the resulting correction to automatic maintenance of a correct posture in the vertical position. The aim of this paper was to discuss the conservative treatment of scoliosis with regard to difficulties maintaining the correct alignment of the body parts in the vertical position that accompany scoliosis.

Contractor Incentives for Success in Implementing Performance-Based Logistics: A Progress Report

DTIC Science & Technology

2010-04-30

amount of risk; this, however, gives the contractor more latitude in determining and applying its methods ( KMC /OPI, 2010). The general consensus...Klevan, P. (2008, October 27). Navy success with PBL. Presentation at the DoD Maintenance Symposium. KMC /OPI. (2010, January 19). Acquisition

Initiating Consensus: Stakeholders Define Entrepreneurship in Education

ERIC Educational Resources Information Center

Omer Attali, Moriah; Yemini, Miri

2017-01-01

While the concept of entrepreneurship in the field of education has received growing scholarly attention in recent years, no consensual definition exists regarding what exactly educational entrepreneurship involves. A clear definition will promote research progress on this subject, as well as its accessibility in the general discourse. The present…

Applying Generalizability Theory for Making Quantitative RTI Progress-Monitoring Decisions

ERIC Educational Resources Information Center

Fan, Chung-Hau; Hansmann, Paul R.

2015-01-01

Language in the Individuals With Disabilities Education Improvement Act (IDEIA) allows the use of response-to-intervention (RTI) methodology in the identification of specific learning disabilities. However, there is no consensus on decision rules using curriculum-based measurement of oral reading fluency (CBM-R) for defining responsiveness. The…

AntiClustal: Multiple Sequence Alignment by antipole clustering and linear approximate 1-median computation.

PubMed

Di Pietro, C; Di Pietro, V; Emmanuele, G; Ferro, A; Maugeri, T; Modica, E; Pigola, G; Pulvirenti, A; Purrello, M; Ragusa, M; Scalia, M; Shasha, D; Travali, S; Zimmitti, V

2003-01-01

In this paper we present a new Multiple Sequence Alignment (MSA) algorithm called AntiClusAl. The method makes use of the commonly use idea of aligning homologous sequences belonging to classes generated by some clustering algorithm, and then continue the alignment process ina bottom-up way along a suitable tree structure. The final result is then read at the root of the tree. Multiple sequence alignment in each cluster makes use of the progressive alignment with the 1-median (center) of the cluster. The 1-median of set S of sequences is the element of S which minimizes the average distance from any other sequence in S. Its exact computation requires quadratic time. The basic idea of our proposed algorithm is to make use of a simple and natural algorithmic technique based on randomized tournaments which has been successfully applied to large size search problems in general metric spaces. In particular a clustering algorithm called Antipole tree and an approximate linear 1-median computation are used. Our algorithm compared with Clustal W, a widely used tool to MSA, shows a better running time results with fully comparable alignment quality. A successful biological application showing high aminoacid conservation during evolution of Xenopus laevis SOD2 is also cited.

Global Surgery System Strengthening: It Is All About the Right Metrics.

PubMed

Watters, David A; Guest, Glenn D; Tangi, Viliami; Shrime, Mark G; Meara, John G

2018-04-01

Progress in achieving "universal access to safe, affordable surgery, and anesthesia care when needed" is dependent on consensus not only about the key messages but also on what metrics should be used to set goals and measure progress. The Lancet Commission on Global Surgery not only achieved consensus on key messages but also recommended 6 key metrics to inform national surgical plans and monitor scale-up toward 2030. These metrics measure access to surgery, as well as its timeliness, safety, and affordability: (1) Two-hour access to the 3 Bellwether procedures (cesarean delivery, emergency laparotomy, and management of an open fracture); (2) Surgeon, Anesthetist, and Obstetrician workforce >20/100,000; (3) Surgical volume of 5000 procedures/100,000; (4) Reporting of perioperative mortality rate; and (5 and 6) Risk rates of catastrophic expenditure and impoverishment when requiring surgery. This article discusses the definition, validity, feasibility, relevance, and progress with each of these metrics. The authors share their experience of introducing the metrics in the Pacific and sub-Saharan Africa. We identify appropriate messages for each potential stakeholder-the patients, practitioners, providers (health services and hospitals), public (community), politicians, policymakers, and payers. We discuss progress toward the metrics being included in core indicator lists by the World Health Organization and the World Bank and how they have been, or may be, used to inform National Surgical Plans in low- and middle-income countries to scale-up the delivery of safe, affordable, and timely surgical and anesthesia care to all who need it.

Development of the Test Of Astronomy STandards (TOAST) Assessment Instrument

NASA Astrophysics Data System (ADS)

Slater, Timothy F.; Slater, S. J.

2008-05-01

Considerable effort in the astronomy education research (AER) community over the past several years has focused on developing assessment tools in the form of multiple-choice conceptual diagnostics and content knowledge surveys. This has been critically important in advancing the AER discipline so that researchers could establish the initial knowledge state of students as well as to attempt measure some of the impacts of innovative instructional interventions. Unfortunately, few of the existing instruments were constructed upon a solid list of clearly articulated and widely agreed upon learning objectives. This was not done in oversight, but rather as a result of the relative youth of AER as a discipline. Now that several important science education reform documents exist and are generally accepted by the AER community, we are in a position to develop, validate, and disseminate a new assessment instrument which is tightly aligned to the consensus learning goals stated by the American Astronomical Society - Chair's Conference on ASTRO 101, the American Association of the Advancement of Science's Project 2061 Benchmarks, and the National Research Council's National Science Education Standards. In response, researchers from the Cognition in Astronomy, Physics and Earth sciences Research (CAPER) Team at the University of Wyoming's Science & Math Teaching Center (UWYO SMTC) have designed a criterion-referenced assessment tool, called the Test Of Astronomy STandards (TOAST). Through iterative development, this instrument has a high degree of reliability and validity for instructors and researchers needing information on students’ initial knowledge state at the beginning of a course and can be used, in aggregate, to help measure the impact of course-length duration instructional strategies for courses with learning goals tightly aligned to the consensus goals of our community.

Reliable Detection of Herpes Simplex Virus Sequence Variation by High-Throughput Resequencing.

PubMed

Morse, Alison M; Calabro, Kaitlyn R; Fear, Justin M; Bloom, David C; McIntyre, Lauren M

2017-08-16

High-throughput sequencing (HTS) has resulted in data for a number of herpes simplex virus (HSV) laboratory strains and clinical isolates. The knowledge of these sequences has been critical for investigating viral pathogenicity. However, the assembly of complete herpesviral genomes, including HSV, is complicated due to the existence of large repeat regions and arrays of smaller reiterated sequences that are commonly found in these genomes. In addition, the inherent genetic variation in populations of isolates for viruses and other microorganisms presents an additional challenge to many existing HTS sequence assembly pipelines. Here, we evaluate two approaches for the identification of genetic variants in HSV1 strains using Illumina short read sequencing data. The first, a reference-based approach, identifies variants from reads aligned to a reference sequence and the second, a de novo assembly approach, identifies variants from reads aligned to de novo assembled consensus sequences. Of critical importance for both approaches is the reduction in the number of low complexity regions through the construction of a non-redundant reference genome. We compared variants identified in the two methods. Our results indicate that approximately 85% of variants are identified regardless of the approach. The reference-based approach to variant discovery captures an additional 15% representing variants divergent from the HSV1 reference possibly due to viral passage. Reference-based approaches are significantly less labor-intensive and identify variants across the genome where de novo assembly-based approaches are limited to regions where contigs have been successfully assembled. In addition, regions of poor quality assembly can lead to false variant identification in de novo consensus sequences. For viruses with a well-assembled reference genome, a reference-based approach is recommended.

A consensus approach to improving patient adherence and persistence with topical treatment for actinic keratosis.

PubMed

Stockfleth, Eggert; Peris, Ketty; Guillen, Carlos; Cerio, Rino; Basset-Seguin, Nicole; Foley, Peter; Sanches, José; Culshaw, Alex; Erntoft, Sandra; Lebwohl, Mark

2015-01-01

Topical therapy is important in the treatment of actinic keratosis, but guidance for improving adherence/persistence during topical therapy is still lacking. To utilize expert consensus to generate a list of recommendations to improve real-world efficacy when prescribing topical therapy for actinic keratosis. An expert panel of eight dermatologists was convened to generate recommendations based on facilitated discussion and consensus generation using a modified Delphi session. The recommendations were ratified with the expert panel. Facilitated discussion generated 31 issues within five themes, which were prioritized using expert voting. Consensus was achieved on the importance of short and simple treatment regimens for maximizing patient compliance, physician awareness of the progression of actinic keratosis to squamous cell carcinoma, provision of appropriate patient information, and the use of effective communication strategies to educate physicians about actinic keratosis. Based on these key findings, eight recommendations were generated. The recommendations will assist physicians when prescribing topical actinic keratosis therapy. Further research should focus on the types of patient outcomes that are influenced by the characteristics of topical field therapy. © 2015 The Authors. International Journal of Dermatology published by John Wiley & Sons Ltd on behalf of International Society of Dermatology.

Universal Health Coverage in Francophone Sub-Saharan Africa: Assessment of Global Health Experts' Confidence in Policy Options.

PubMed

Paul, Elisabeth; Fecher, Fabienne; Meloni, Remo; van Lerberghe, Wim

2018-05-29

Many countries rely on standard recipes for accelerating progress toward universal health coverage (UHC). With limited generalizable empirical evidence, expert confidence and consensus plays a major role in shaping country policy choices. This article presents an exploratory attempt conducted between April and September 2016 to measure confidence and consensus among a panel of global health experts in terms of the effectiveness and feasibility of a number of policy options commonly proposed for achieving UHC in low- and middle-income countries, such as fee exemptions for certain groups of people, ring-fenced domestic health budgets, and public-private partnerships. To ensure a relative homogeneity of contexts, we focused on French-speaking sub-Saharan Africa. We initially used the Delphi method to arrive at expert consensus, but since no consensus emerged after 2 rounds, we adjusted our approach to a statistical analysis of the results from our questionnaire by measuring the degree of consensus on each policy option through 100 (signifying total consensus) minus the size of the interquartile range of the individual scores. Seventeen global health experts from various backgrounds, but with at least 20 years' experience in the broad region, participated in the 2 rounds of the study. The results provide an initial "mapping" of the opinions of a group of experts and suggest interesting lessons. For the 18 policy options proposed, consensus emerged only on strengthening the supply of quality primary health care services (judged as being effective with a confidence score of 79 and consensus score of 90), and on fee exemptions for the poorest (judged as being fairly easy to implement with a confidence score of 66 and consensus score of 85). For none of the 18 common policy options was there consensus on both potential effectiveness and feasibility, with very diverging opinions concerning 5 policy options. The lack of confidence and consensus within the panel seems to reflect the lack of consistent evidence on the proposed policy options. This suggests that experts' opinions should be framed within strengthened inclusive and "evidence-informed deliberative processes" where the trade-offs along the 3 dimensions of UHC-extending the population covered against health hazards, expanding the range of services and benefits covered, and reducing out-of-pocket expenditures-can be discussed in a transparent and contextualized setting. © Paul et al.

Fear of progression.

PubMed

Herschbach, Peter; Dinkel, Andreas

2014-01-01

Fear of progression (or fear of recurrence) is an appropriate, rational response to the real threat of cancer and cancer treatments. However, elevated levels of fear of progression can become dysfunctional, affecting well-being, quality of life, and social functioning. Research has shown that fear of progression is one of the most frequent distress symptoms of patients with cancer and with other chronic diseases. As a clear consensus concerning clinically relevant states of fear of progression is currently lacking, it is difficult to provide a valid estimate of the rate of cancer patients who clearly suffer from fear of progression. However, recent systematic reviews suggest that probably 50 % of cancer patients experience moderate to severe fear of progression. Furthermore, many patients express unmet needs in dealing with the fear of cancer spreading. These results underline the necessity to provide effective psychological treatments for clinical levels of fear of progression. A few psychosocial interventions for treating fear of progression have been developed so far. Our own, targeted intervention study showed that dysfunctional fear of progression can be effectively treated with a brief group therapy.

Technology-enabled assessment of health professions education: consensus statement and recommendations from the Ottawa 2010 Conference.

PubMed

Amin, Zubair; Boulet, John R; Cook, David A; Ellaway, Rachel; Fahal, Ahmad; Kneebone, Roger; Maley, Moira; Ostergaard, Doris; Ponnamperuma, Gominda; Wearn, Andy; Ziv, Amitai

2011-01-01

The uptake of information and communication technologies (ICTs) in health professions education can have far-reaching consequences on assessment. The medical education community still needs to develop a deeper understanding of how technology can underpin and extend assessment practices. This article was developed by the 2010 Ottawa Conference Consensus Group on technology-enabled assessment to guide practitioners and researchers working in this area. This article highlights the changing nature of ICTs in assessment, the importance of aligning technology-enabled assessment with local context and needs, the need for better evidence to support use of technologies in health profession education assessment, and a number of challenges, particularly validity threats, that need to be addressed while incorporating technology in assessment. Our recommendations are intended for all practitioners across health professional education. Recommendations include adhering to principles of good assessment, the need for developing coherent institutional policy, using technologies to broaden the competencies to be assessed, linking patient-outcome data to assessment of practitioner performance, and capitalizing on technologies for the management of the entire life-cycle of assessment.

Report on Progress Toward Security and Stability in Afghanistan

DTIC Science & Technology

2010-11-01

National Governance Policy The Sub National Governance ( SNG ) Policy establishes a framework for instituting government reforms over the next 15 years.34...governance and development initiatives, such as the National Solidarity Program and the Afghan Social Outreach Program, align with the new SNG policy...review implementation progress from a financing perspective. 4. Municipal governance - A key component of the SNG policy reform will be to draft a

A Study of the Alignment between the NAEP Mathematics Framework and the Common Core State Standards for Mathematics (CCSS-M)

ERIC Educational Resources Information Center

Hughes, Gerunda B.; Daro, Phil; Holtzman, Deborah; Middleton, Kyndra

2013-01-01

Introduction: For decades, prior to the inception of the Common Core State Standards (CCSS), the National Assessment of Educational Progress (NAEP) was the only vehicle through which states could assess the progress of their students using a common metric. Now, 45 states, 4 U.S. territories, and the District of Columbia have adopted the CCSS to…

Definition and classification of cancer cachexia: an international consensus.

PubMed

Fearon, Kenneth; Strasser, Florian; Anker, Stefan D; Bosaeus, Ingvar; Bruera, Eduardo; Fainsinger, Robin L; Jatoi, Aminah; Loprinzi, Charles; MacDonald, Neil; Mantovani, Giovanni; Davis, Mellar; Muscaritoli, Maurizio; Ottery, Faith; Radbruch, Lukas; Ravasco, Paula; Walsh, Declan; Wilcock, Andrew; Kaasa, Stein; Baracos, Vickie E

2011-05-01

To develop a framework for the definition and classification of cancer cachexia a panel of experts participated in a formal consensus process, including focus groups and two Delphi rounds. Cancer cachexia was defined as a multifactorial syndrome defined by an ongoing loss of skeletal muscle mass (with or without loss of fat mass) that cannot be fully reversed by conventional nutritional support and leads to progressive functional impairment. Its pathophysiology is characterised by a negative protein and energy balance driven by a variable combination of reduced food intake and abnormal metabolism. The agreed diagnostic criterion for cachexia was weight loss greater than 5%, or weight loss greater than 2% in individuals already showing depletion according to current bodyweight and height (body-mass index [BMI] <20 kg/m(2)) or skeletal muscle mass (sarcopenia). An agreement was made that the cachexia syndrome can develop progressively through various stages--precachexia to cachexia to refractory cachexia. Severity can be classified according to degree of depletion of energy stores and body protein (BMI) in combination with degree of ongoing weight loss. Assessment for classification and clinical management should include the following domains: anorexia or reduced food intake, catabolic drive, muscle mass and strength, functional and psychosocial impairment. Consensus exists on a framework for the definition and classification of cancer cachexia. After validation, this should aid clinical trial design, development of practice guidelines, and, eventually, routine clinical management. Copyright © 2011 Elsevier Ltd. All rights reserved.

Prevention and treatment of tuberculosis infection in candidates for biologic therapy: A multidisciplinary consensus statement adapted to the dermatology patient.

PubMed

Rodríguez-Jiménez, P; Mir-Viladrich, I; Chicharro, P; Solano-López, G; López-Longo, F J; Taxonera, C; Sánchez-Martínez, P; Martínez-Lacasa, X; García-Gasalla, M; Dorca, J; Arias-Guillén, M; García-García, J M; Dauden, E

2018-06-02

Patients with chronic inflammatory diseases being treated with immunosuppressive drugs, and with tumor necrosis factor inhibitors in particular, have an increased risk of infection by Mycobacterium tuberculosis. Screening for latent tuberculosis infection and preventive therapy to reduce the risk of progression to active tuberculosis are mandatory in this group of patients. This updated multidisciplinary consensus document presents the latest expert opinions on the treatment and prevention of tuberculosis in candidates for biologic therapy and establishes recommendations based on current knowledge relating to the use of biologic agents. Copyright © 2018 AEDV. Publicado por Elsevier España, S.L.U. All rights reserved.

[Acute respiratory distress syndrome in childhood: Changing definition and news from the Pediatric Consensus Conference].

PubMed

Dauger, S; Le Bourgeois, F; Guichoux, J; Brissaud, O

2017-05-01

Acute respiratory distress syndrome (ARDS) is a rapidly progressive hypoxemic respiratory insufficiency induced by alveolar filling mainly caused by alveolocapillary wall disruption, following direct or indirect pulmonary injury. Much less frequent in children than in adults, pediatric intensivists had long applied adult guidelines to their daily practice. In 2015, experts from the Pediatric Acute Lung Injury Consensus Conference (PALICC) published the first international guidelines specifically dedicated to pediatric ARDS. After a short summary of the history of the ARDS definition since its first report in 1967, we describe the main diagnostic and therapeutic guidelines for PALICC. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Consensus Document on Prevention and Treatment of Tuberculosis in Patients for Biological Treatment.

PubMed

Mir Viladrich, Isabel; Daudén Tello, Esteban; Solano-López, Guillermo; López Longo, Francisco Javier; Taxonera Samso, Carlos; Sánchez Martínez, Paquita; Martínez Lacasa, Xavier; García Gasalla, Mercedes; Dorca Sargatal, Jordi; Arias-Guillén, Miguel; García García, José Maria

2016-01-01

Tuberculosis risk is increased in patients with chronic inflammatory diseases receiving any immunosuppressive treatment, notably tumor necrosis factor (TNF) antagonists therapy. Screening for the presence of latent infection with Mycobacterium tuberculosis and targeted preventive treatment to reduce the risk of progression to TB is mandatory in these patients. This Consensus Document summarizes the current knowledge and expert opinion of biologic therapies including TNF-blocking treatments. It provides recommendations for the use of interferon-gamma release assays (IGRA) and tuberculin skin test (TST) for the diagnosis of latent tuberculosis infection in these patients, and for the type and duration of preventive therapy. Copyright © 2015 SEPAR. Published by Elsevier Espana. All rights reserved.

Toward Active X-ray Telescopes II

NASA Technical Reports Server (NTRS)

O'Dell, Stephen L.; Aldroft, Thomas L.; Atkins, Carolyn; Button, Timothy W.; Cotroneo, Vincenzo; Davis, William N.; Doel, Peter; Feldman, Charlotte H.; Freeman, Mark D.; Gubarev, Mikhail V.;

78 FR 55135 - Request for Comments on Additional Participants in Trade in Services Agreement

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-09

... Congress of the Administration's intention to enter into negotiations for a Trade in Services Agreement... negotiating TISA ``will expand as negotiations progress to include others who share our ambitious goals. This... consensus to allow these new participants to join the negotiations. The Office of the United States Trade...

Neurobiology of Childhood-Onset Schizophrenia

ERIC Educational Resources Information Center

Biswas, Parthasarathy

2008-01-01

In the last decade there has been an exponential increase in studies on neurobiological measures in childhood-onset schizophrenia (COS). There seems to be a consensus that structural changes in COS are more marked than in adolescence-onset (AdOS) or adult-onset schizophrenia (AOS). Atrophy of total brain volume is progressive throughout the course…

Content-Related Knowledge of Biology Teachers from Secondary Schools: Structure and Learning Opportunities

ERIC Educational Resources Information Center

Großschedl, Jörg; Mahler, Daniela; Kleickmann, Thilo; Harms, Ute

2014-01-01

Teachers' content-related knowledge is a key factor influencing the learning progress of students. Different models of content-related knowledge have been proposed by educational researchers; most of them take into account three categories: content knowledge, pedagogical content knowledge, and curricular knowledge. As there is no consensus about…

Biological Markers of Cognition in Prodromal Huntington's Disease: A Review

ERIC Educational Resources Information Center

Papp, Kathryn V.; Kaplan, Richard F.; Snyder, Peter J.

2011-01-01

Huntington's disease (HD), an autosomal-dominant genetic disorder, has historically been viewed as a degenerative movement disorder but it also includes psychiatric symptoms and progressive cognitive decline. There has been a lack of consensus in the literature about whether or not cognitive signs can be detected in carriers before clinical…

Contributions of Social-Emotional Readiness and Classroom Quality to Social-Emotional Trajectories across Elementary School

ERIC Educational Resources Information Center

Abenavoli, Rachel M.; Greenberg, Mark T.

2016-01-01

There is growing consensus among researchers and practitioners that children's socialemotional readiness makes unique contributions to their successful transition to and progress through school. However, many children still begin school ill-prepared for the behavioral demands they will encounter in the classroom. This study examines the joint…

Community Vision and Interagency Alignment: A Community Planning Process to Promote Active Transportation

PubMed Central

Chaudhury, Nupur; Kennedy, Patrick; Noyes, Philip; Maybank, Aletha

2016-01-01

In 2010, the Brooklyn Active Transportation Community Planning Initiative launched in 2 New York City neighborhoods. Over a 2-year planning period, residents participated in surveys, school and community forums, neighborhood street assessments, and activation events—activities that highlighted the need for safer streets locally. Consensus among residents and key multisectoral stakeholders, including city agencies and community-based organizations, was garnered in support of a planned expansion of bicycling infrastructure. The process of building on community assets and applying a collective impact approach yielded changes in the built environment, attracted new partners and resources, and helped to restore a sense of power among residents. PMID:26959270

Community Vision and Interagency Alignment: A Community Planning Process to Promote Active Transportation.

PubMed

DeGregory, Sarah Timmins; Chaudhury, Nupur; Kennedy, Patrick; Noyes, Philip; Maybank, Aletha

2016-04-01

In 2010, the Brooklyn Active Transportation Community Planning Initiative launched in 2 New York City neighborhoods. Over a 2-year planning period, residents participated in surveys, school and community forums, neighborhood street assessments, and activation events-activities that highlighted the need for safer streets locally. Consensus among residents and key multisectoral stakeholders, including city agencies and community-based organizations, was garnered in support of a planned expansion of bicycling infrastructure. The process of building on community assets and applying a collective impact approach yielded changes in the built environment, attracted new partners and resources, and helped to restore a sense of power among residents.

What should DOE do to help establish voluntary consensus standards for measuring and rating the performance of PV modules?

NASA Technical Reports Server (NTRS)

Runkle, L. D.

1984-01-01

In response to concern expressed by the photovoltaics community over progress toward the establishment and issuance of concensus standards on photovoltaic performance measurements, a review of the status of and progress in developing these standards was conducted. It examined the roles of manufacturers, and consumers and the national laboratories funded by the U.S. Department of Energy (DOE) in supporting this effort. This was done by means of a series of discussions with knowledgeable members of the photovoltaic community. Results of these interviews are summarized and a new approach to managing support of standards activity is recommended that responds to specific problems found in the performance measurement standards area. The study concludes that there is a positive role to be played by the U.S. Department of Energy in establishing collector performance measurement standards. It recommends that DOE continue to provide direct financial support for selected committees and for research at national laboratories, and that management of the activity be restructured to increase the authority and responsibility of the consensus committees.

The patient's progress from this world to that which is to come: commentary on the Consensus Statement of the Working Group on Roman Catholic Approaches to Determining Critical Care.

PubMed

Schmidt, K W

2001-08-01

The author comments on the consensus statement from the point of view of an ethics consultant in Germany. Since many hospitals in Germany are under considerable competitive pressure, mission statements are becoming more and more important in order to draw a distinction between the different hospital types and to convey the meaning of the corporate identity both internally and externally. The Consensus Statement, which provides basic orientation without going into too much detail, can be a helpful initial document. However, it does not deal with two specific problem areas which are examined more closely in the commentary: the application of risk-of-death algorithims in ICUs and the question of church membership of the caregivers to enable a proper preparation for death. The commentary also reveals certain difficulties in the discussion taking place in Anglo-Saxon countries and Continental Europe.

Expert Consensus for Discharge Referral Decisions Using Online Delphi

PubMed Central

Bowles, Kathy H.; Holmes, John H.; Naylor, Mary D.; Liberatore, Matthew; Nydick, Robert

2003-01-01

This paper describes the results of using a modified Delphi approach designed to achieve consensus from eight discharge planning experts regarding the decision to refer hospitalized older adults for post-discharge follow-up. Experts reviewed 150 cases using an online website designed to facilitate their interaction and efforts to reach agreement on the need for a referral for post-discharge care and the appropriate site for such care. In contrast to an average of eight weeks to complete just 50 cases using the traditional mail method, the first online Delphi round for 150 cases were completed in six weeks. Data provided by experts suggest that online Delphi is a time efficient and acceptable methodology for reaching group consensus. Other benefits include instant access to Delphi decision results, live knowledge of the time requirements and progress of each expert, and cost savings in postage, paper, copying, and storage of paper documents. This online Delphi methodology is highly recommended. PMID:14728143

A consensus action agenda for achieving the national health information infrastructure.

PubMed

Yasnoff, William A; Humphreys, Betsy L; Overhage, J Marc; Detmer, Don E; Brennan, Patricia Flatley; Morris, Richard W; Middleton, Blackford; Bates, David W; Fanning, John P

2004-01-01

Improving the safety, quality, and efficiency of health care will require immediate and ubiquitous access to complete patient information and decision support provided through a National Health Information Infrastructure (NHII). To help define the action steps needed to achieve an NHII, the U.S. Department of Health and Human Services sponsored a national consensus conference in July 2003. Attendees favored a public-private coordination group to guide NHII activities, provide education, share resources, and monitor relevant metrics to mark progress. They identified financial incentives, health information standards, and overcoming a few important legal obstacles as key NHII enablers. Community and regional implementation projects, including consumer access to a personal health record, were seen as necessary to demonstrate comprehensive functional systems that can serve as models for the entire nation. Finally, the participants identified the need for increased funding for research on the impact of health information technology on patient safety and quality of care. Individuals, organizations, and federal agencies are using these consensus recommendations to guide NHII efforts.

Consensus Statement on Standard of Care for Congenital Myopathies

PubMed Central

Wang, Ching H.; Dowling, James J.; North, Kathryn; Schroth, Mary K.; Sejersen, Thomas; Shapiro, Frederic; Bellini, Jonathan; Weiss, Hali; Guillet, Marc; Amburgey, Kimberly; Apkon, Susan; Bertini, Enrico; Bonnemann, Carsten; Clarke, Nigel; Connolly, Anne M.; Estournet-Mathiaud, Brigitte; Fitzgerald, Dominic; Florence, Julaine M.; Gee, Richard; Gurgel-Giannetti, Juliana; Glanzman, Allan M.; Hofmeister, Brittany; Jungbluth, Heinz; Koumbourlis, Anastassios C.; Laing, Nigel G.; Main, Marion; Morrison, Leslie A.; Munns, Craig; Rose, Kristy; Schuler, Pamela M.; Sewry, Caroline; Storhaug, Kari; Vainzof, Mariz; Yuan, Nanci

2016-01-01

Recent progress in scientific research has facilitated accurate genetic and neuropathological diagnosis of congenital myopathies. However, given their relatively low incidence, congenital myopathies remain unfamiliar to the majority of care providers, and the levels of patient care are extremely variable. This consensus statement aims to provide care guidelines for congenital myopathies. The International Standard of Care Committee for Congenital Myopathies worked through frequent e-mail correspondences, periodic conference calls, 2 rounds of online surveys, and a 3-day workshop to achieve a consensus for diagnostic and clinical care recommendations. The committee includes 59 members from 10 medical disciplines. They are organized into 5 working groups: genetics/diagnosis, neurology, pulmonology, gastroenterology/nutrition/speech/oral care, and orthopedics/rehabilitation. In each care area the authors summarize the committee’s recommendations for symptom assessments and therapeutic interventions. It is the committee’s goal that through these recommendations, patients with congenital myopathies will receive optimal care and improve their disease outcome. PMID:22431881

Development of a low loss magnetic composite utilizing amorphous metal flake. Second semi-annual progress report, March 19-September 18, 1979

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

Not Available

1979-10-01

Composite specimens of amorphous metal flakes have been made using several different binders and several different compaction parameters. The binders have included epoxies, anaerobic adhesives, polyimides, polyamideimides, polyeherimides, and polyesterimides. Compaction variables included the time, temperature and pressure of compaction; flake size, and flake alignment. The best results were achieved using a polyetherimide and aligned flake. Packing factors of 87% were achieved in specimens which also exhibited high mechanical integrity and the ability to withstand a high temperature anneal.

Protein alignment algorithms with an efficient backtracking routine on multiple GPUs.

PubMed

Blazewicz, Jacek; Frohmberg, Wojciech; Kierzynka, Michal; Pesch, Erwin; Wojciechowski, Pawel

2011-05-20

Pairwise sequence alignment methods are widely used in biological research. The increasing number of sequences is perceived as one of the upcoming challenges for sequence alignment methods in the nearest future. To overcome this challenge several GPU (Graphics Processing Unit) computing approaches have been proposed lately. These solutions show a great potential of a GPU platform but in most cases address the problem of sequence database scanning and computing only the alignment score whereas the alignment itself is omitted. Thus, the need arose to implement the global and semiglobal Needleman-Wunsch, and Smith-Waterman algorithms with a backtracking procedure which is needed to construct the alignment. In this paper we present the solution that performs the alignment of every given sequence pair, which is a required step for progressive multiple sequence alignment methods, as well as for DNA recognition at the DNA assembly stage. Performed tests show that the implementation, with performance up to 6.3 GCUPS on a single GPU for affine gap penalties, is very efficient in comparison to other CPU and GPU-based solutions. Moreover, multiple GPUs support with load balancing makes the application very scalable. The article shows that the backtracking procedure of the sequence alignment algorithms may be designed to fit in with the GPU architecture. Therefore, our algorithm, apart from scores, is able to compute pairwise alignments. This opens a wide range of new possibilities, allowing other methods from the area of molecular biology to take advantage of the new computational architecture. Performed tests show that the efficiency of the implementation is excellent. Moreover, the speed of our GPU-based algorithms can be almost linearly increased when using more than one graphics card.

Comparison of ZP3 protein sequences among vertebrate species: to obtain a consensus sequence for immunocontraception.

PubMed

Zhu, X; Naz, R K

1999-03-01

The deduced ZP3 amino acid (aa) sequences of 13 vertebrate species namely mouse, hamster, rabbit, pig, porcine, cow, dog, cat, human, bonnet, marmoset, carp, and frog were compared using the PILEUP and PRETTY alignment programs (GCG, Wisconsin, USA). The published aa sequences obtained from 13 vertebrate species indicated the overall evolutionarily conservation in the N-terminus, central region, and C-terminus of the ZP3 polypeptide. More variations of ZP3 polypeptide sequences were seen in the alignments of carp and frog from the 11 mammalian species making the leader sequence more prominent. The canonical furin proteolytic processing signal at the C-terminus was found in all the ZP3 polypeptide sequences except of carp and frog. In the central region, the ZP3 deduced aa sequences of all the 13 vertebrate species aligned well, and six relatively conserved sequences were found. There are 11 conserved cysteine residues in the central region across all species including carp and frog, indicating that these residues have longer evolutionary history. The ZP3 aa sequence similarities were examined using the GAP program (GCG). The highest aa similarities are observed between the members of the same order within the class mammalia, and also (95.4%) between pig (ungulata) and rabbit (lagomorpha). The deduced ZP3 aa sequences per se may not be enough to build a phylogenetic tree.

Visualizing bacterial tRNA identity determinants and antideterminants using function logos and inverse function logos

PubMed Central

Freyhult, Eva; Moulton, Vincent; Ardell, David H.

2006-01-01

Sequence logos are stacked bar graphs that generalize the notion of consensus sequence. They employ entropy statistics very effectively to display variation in a structural alignment of sequences of a common function, while emphasizing its over-represented features. Yet sequence logos cannot display features that distinguish functional subclasses within a structurally related superfamily nor do they display under-represented features. We introduce two extensions to address these needs: function logos and inverse logos. Function logos display subfunctions that are over-represented among sequences carrying a specific feature. Inverse logos generalize both sequence logos and function logos by displaying under-represented, rather than over-represented, features or functions in structural alignments. To make inverse logos, a compositional inverse is applied to the feature or function frequency distributions before logo construction, where a compositional inverse is a mathematical transform that makes common features or functions rare and vice versa. We applied these methods to a database of structurally aligned bacterial tDNAs to create highly condensed, birds-eye views of potentially all so-called identity determinants and antideterminants that confer specific amino acid charging or initiator function on tRNAs in bacteria. We recovered both known and a few potentially novel identity elements. Function logos and inverse logos are useful tools for exploratory bioinformatic analysis of structure–function relationships in sequence families and superfamilies. PMID:16473848

FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe.

PubMed

Gertz, E Michael; Chowdhury, Salim Akhter; Lee, Woei-Jyh; Wangsa, Darawalee; Heselmeyer-Haddad, Kerstin; Ried, Thomas; Schwartz, Russell; Schäffer, Alejandro A

2016-01-01

Advances in fluorescence in situ hybridization (FISH) make it feasible to detect multiple copy-number changes in hundreds of cells of solid tumors. Studies using FISH, sequencing, and other technologies have revealed substantial intra-tumor heterogeneity. The evolution of subclones in tumors may be modeled by phylogenies. Tumors often harbor aneuploid or polyploid cell populations. Using a FISH probe to estimate changes in ploidy can guide the creation of trees that model changes in ploidy and individual gene copy-number variations. We present FISHtrees 3.0, which implements a ploidy-based tree building method based on mixed integer linear programming (MILP). The ploidy-based modeling in FISHtrees includes a new formulation of the problem of merging trees for changes of a single gene into trees modeling changes in multiple genes and the ploidy. When multiple samples are collected from each patient, varying over time or tumor regions, it is useful to evaluate similarities in tumor progression among the samples. Therefore, we further implemented in FISHtrees 3.0 a new method to build consensus graphs for multiple samples. We validate FISHtrees 3.0 on a simulated data and on FISH data from paired cases of cervical primary and metastatic tumors and on paired breast ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC). Tests on simulated data show improved accuracy of the ploidy-based approach relative to prior ploidyless methods. Tests on real data further demonstrate novel insights these methods offer into tumor progression processes. Trees for DCIS samples are significantly less complex than trees for paired IDC samples. Consensus graphs show substantial divergence among most paired samples from both sets. Low consensus between DCIS and IDC trees may help explain the difficulty in finding biomarkers that predict which DCIS cases are at most risk to progress to IDC. The FISHtrees software is available at ftp://ftp.ncbi.nih.gov/pub/FISHtrees.

Assessing Genetic Structure in Common but Ecologically Distinct Carnivores: The Stone Marten and Red Fox.

PubMed

Basto, Mafalda P; Santos-Reis, Margarida; Simões, Luciana; Grilo, Clara; Cardoso, Luís; Cortes, Helder; Bruford, Michael W; Fernandes, Carlos

2016-01-01

The identification of populations and spatial genetic patterns is important for ecological and conservation research, and spatially explicit individual-based methods have been recognised as powerful tools in this context. Mammalian carnivores are intrinsically vulnerable to habitat fragmentation but not much is known about the genetic consequences of fragmentation in common species. Stone martens (Martes foina) and red foxes (Vulpes vulpes) share a widespread Palearctic distribution and are considered habitat generalists, but in the Iberian Peninsula stone martens tend to occur in higher quality habitats. We compared their genetic structure in Portugal to see if they are consistent with their differences in ecological plasticity, and also to illustrate an approach to explicitly delineate the spatial boundaries of consistently identified genetic units. We analysed microsatellite data using spatial Bayesian clustering methods (implemented in the software BAPS, GENELAND and TESS), a progressive partitioning approach and a multivariate technique (Spatial Principal Components Analysis-sPCA). Three consensus Bayesian clusters were identified for the stone marten. No consensus was achieved for the red fox, but one cluster was the most probable clustering solution. Progressive partitioning and sPCA suggested additional clusters in the stone marten but they were not consistent among methods and were geographically incoherent. The contrasting results between the two species are consistent with the literature reporting stricter ecological requirements of the stone marten in the Iberian Peninsula. The observed genetic structure in the stone marten may have been influenced by landscape features, particularly rivers, and fragmentation. We suggest that an approach based on a consensus clustering solution of multiple different algorithms may provide an objective and effective means to delineate potential boundaries of inferred subpopulations. sPCA and progressive partitioning offer further verification of possible population structure and may be useful for revealing cryptic spatial genetic patterns worth further investigation.

FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe

PubMed Central

Chowdhury, Salim Akhter; Lee, Woei-Jyh; Wangsa, Darawalee; Heselmeyer-Haddad, Kerstin; Ried, Thomas; Schwartz, Russell; Schäffer, Alejandro A.

2016-01-01

Advances in fluorescence in situ hybridization (FISH) make it feasible to detect multiple copy-number changes in hundreds of cells of solid tumors. Studies using FISH, sequencing, and other technologies have revealed substantial intra-tumor heterogeneity. The evolution of subclones in tumors may be modeled by phylogenies. Tumors often harbor aneuploid or polyploid cell populations. Using a FISH probe to estimate changes in ploidy can guide the creation of trees that model changes in ploidy and individual gene copy-number variations. We present FISHtrees 3.0, which implements a ploidy-based tree building method based on mixed integer linear programming (MILP). The ploidy-based modeling in FISHtrees includes a new formulation of the problem of merging trees for changes of a single gene into trees modeling changes in multiple genes and the ploidy. When multiple samples are collected from each patient, varying over time or tumor regions, it is useful to evaluate similarities in tumor progression among the samples. Therefore, we further implemented in FISHtrees 3.0 a new method to build consensus graphs for multiple samples. We validate FISHtrees 3.0 on a simulated data and on FISH data from paired cases of cervical primary and metastatic tumors and on paired breast ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC). Tests on simulated data show improved accuracy of the ploidy-based approach relative to prior ploidyless methods. Tests on real data further demonstrate novel insights these methods offer into tumor progression processes. Trees for DCIS samples are significantly less complex than trees for paired IDC samples. Consensus graphs show substantial divergence among most paired samples from both sets. Low consensus between DCIS and IDC trees may help explain the difficulty in finding biomarkers that predict which DCIS cases are at most risk to progress to IDC. The FISHtrees software is available at ftp://ftp.ncbi.nih.gov/pub/FISHtrees. PMID:27362268

[Consensus on the detection and management of prediabetes. Consensus and Clinical Guidelines Working Group of the Spanish Diabetes Society].

PubMed

Mata-Cases, M; Artola, S; Escalada, J; Ezkurra-Loyola, P; Ferrer-García, J C; Fornos, J A; Girbés, J; Rica, I

2015-03-01

In Spain, according to the Di@bet.es study, 13.8% of the adult population suffers from diabetes and 14.8% from some form of prediabetes (impaired glucose tolerance, impaired fasting glucose or both). Since early detection of prediabetes can facilitate the implementation of therapeutic measures to prevent its progression to diabetes, we believe that preventive strategies in primary care and specialized clinical settings should be agreed. Screening for diabetes and prediabetes using a specific questionnaire (FINDRISC) and/or the measurement of fasting plasma glucose in high risk patients leads to detecting patients at risk of developing diabetes and it is necessary to consider how they should be managed. The intervention in lifestyle can reduce the progression to diabetes and reverse a prediabetic state to normal and is a cost-effective intervention. Some drugs, such as metformin, have also been shown effective in reducing the progression to diabetes but are not superior to non-pharmacological interventions. Finally, an improvement in some cardiovascular risk factors has been observed although there is no strong evidence supporting the effectiveness of screening in terms of morbility and mortality. The Consensus and Clinical Guidelines Working Group of the Spanish Diabetes Society has issued some recommendations that have been agreed by the Sociedad Española de Endocrinología y Nutrición, Sociedad Española de Endocrinología Pediátrica, Sociedad Española de Farmacia Comunitaria, Sociedad Española de Medicina Familiar y Comunitaria, Sociedad Española de Médicos Generales, Sociedad Española de Médicos de Atención Primaria, Sociedad Española de Medicina Interna, Asociación de Enfermería Comunitaria and Red de Grupos de Estudio de la Diabetes en Atención Primaria. Copyright © 2014 SEEN. Published by Elsevier España, S.L.U. All rights reserved.

Consensus on the detection and management of prediabetes. Consensus and Clinical Guidelines Working Group of the Spanish Diabetes Society.

PubMed

Mata-Cases, M; Artola, S; Escalada, J; Ezkurra-Loyola, P; Ferrer-García, J C; Fornos, J A; Girbés, J; Rica, I

2015-03-01

In Spain, according to the Di@bet.es study, 13.8% of the adult population suffers from diabetes and 14.8% from some form of prediabetes (impaired glucose tolerance, impaired fasting glucose or both). Since early detection of prediabetes can facilitate the implementation of therapeutic measures to prevent its progression to diabetes, we believe that preventive strategies in primary care and specialized clinical settings should be agreed. Screening for diabetes and prediabetes using a specific questionnaire (FINDRISC) and/or the measurement of fasting plasma glucose in high risk patients leads to detecting patients at risk of developing diabetes and it is necessary to consider how they should be managed. The intervention in lifestyle can reduce the progression to diabetes and reverse a prediabetic state to normal and is a cost-effective intervention. Some drugs, such as metformin, have also been shown effective in reducing the progression to diabetes but are not superior to non-pharmacological interventions. Finally, an improvement in some cardiovascular risk factors has been observed although there is no strong evidence supporting the effectiveness of screening in terms of morbility and mortality. The Consensus and Clinical Guidelines Working Group of the Spanish Diabetes Society has issued some recommendations that have been agreed by the Sociedad Española de Endocrinología y Nutrición, Sociedad Española de Endocrinología Pediátrica, Sociedad Española de Farmacia Comunitaria, Sociedad Española de Medicina Familiar y Comunitaria, Sociedad Española de Médicos Generales, Sociedad Española de Médicos de Atención Primaria, Sociedad Española de Medicina Interna, Asociación de Enfermería Comunitaria and Red de Grupos de Estudio de la Diabetes en Atención Primaria. Copyright © 2014 Elsevier España, S.L.U. All rights reserved.

[Consensus on the detection and management of prediabetes. Consensus and Clinical Guidelines Working Group of the Spanish Diabetes Society].

PubMed

Mata-Cases, M; Artola, S; Escalada, J; Ezkurra-Loyola, P; Ferrer-García, J C; Fornos, J A; Girbés, J; Rica, I

2015-01-01

In Spain, according to the Di@bet.es study, 13.8% of the adult population suffers from diabetes and 14.8% from some form of prediabetes (impaired glucose tolerance, impaired fasting glucose or both). Since early detection of prediabetes can facilitate the implementation of therapeutic measures to prevent its progression to diabetes, we believe that preventive strategies in primary care and specialized clinical settings should be agreed. Screening for diabetes and prediabetes using a specific questionnaire (FINDRISC) and/or the measurement of fasting plasma glucose in high risk patients leads to detecting patients at risk of developing diabetes and it is necessary to consider how they should be managed. The intervention in lifestyle can reduce the progression to diabetes and reverse a prediabetic state to normal and is a cost-effective intervention. Some drugs, such as metformin, have also been shown effective in reducing the progression to diabetes but are not superior to non-pharmacological interventions. Finally, an improvement in some cardiovascular risk factors has been observed although there is no strong evidence supporting the effectiveness of screening in terms of morbility and mortality. The Consensus and Clinical Guidelines Working Group of the Spanish Diabetes Society has issued some recommendations that have been agreed by the Sociedad Española de Endocrinología y Nutrición, Sociedad Española de Endocrinología Pediátrica, Sociedad Española de Farmacia Comunitaria, Sociedad Española de Medicina Familiar y Comunitaria, Sociedad Española de Médicos Generales, Sociedad Española de Médicos de Atención Primaria, Sociedad Española de Medicina Interna, Asociación de Enfermería Comunitaria and Red de Grupos de Estudio de la Diabetes en Atención Primaria. Copyright © 2015. Publicado por Elsevier España, S.L.U.

[Consensus on the detection and management of prediabetes. Consensus and Clinical Guidelines Working Group of the Spanish Diabetes Society].

PubMed

Mata-Cases, M; Artola, S; Escalada, J; Ezkurra-Loyola, P; Ferrer-García, J C; Fornos, J A; Girbés, J; Rica, I

2015-01-01

In Spain, according to the Di@bet.es study, 13.8% of the adult population suffers from diabetes and 14.8% from some form of prediabetes (impaired glucose tolerance, impaired fasting glucose or both). Since early detection of prediabetes can facilitate the implementation of therapeutic measures to prevent its progression to diabetes, we believe that preventive strategies in primary care and specialized clinical settings should be agreed. Screening for diabetes and prediabetes using a specific questionnaire (FINDRISC) and/or the measurement of fasting plasma glucose in high risk patients leads to detecting patients at risk of developing diabetes and it is necessary to consider how they should be managed. The intervention in lifestyle can reduce the progression to diabetes and reverse a prediabetic state to normal and is a cost-effective intervention. Some drugs, such as metformin, have also been shown effective in reducing the progression to diabetes but are not superior to non-pharmacological interventions. Finally, an improvement in some cardiovascular risk factors has been observed although there is no strong evidence supporting the effectiveness of screening in terms of morbility and mortality. The Consensus and Clinical Guidelines Working Group of the Spanish Diabetes Society has issued some recommendations that have been agreed by the Sociedad Española de Endocrinología y Nutrición, Sociedad Española de Endocrinología Pediátrica, Sociedad Española de Farmacia Comunitaria, Sociedad Española de Medicina Familiar y Comunitaria, Sociedad Española de Médicos Generales, Sociedad Española de Médicos de Atención Primaria, Sociedad Española de Medicina Interna, Asociación de Enfermería Comunitaria and Red de Grupos de Estudio de la Diabetes en Atención Primaria. Copyright © 2014 Sociedad Española de Médicos de Atención Primaria (SEMERGEN). Publicado por Elsevier España, S.L.U. All rights reserved.

Assessing Genetic Structure in Common but Ecologically Distinct Carnivores: The Stone Marten and Red Fox

PubMed Central

Basto, Mafalda P.; Santos-Reis, Margarida; Simões, Luciana; Grilo, Clara; Cardoso, Luís; Cortes, Helder; Bruford, Michael W.; Fernandes, Carlos

2016-01-01

The identification of populations and spatial genetic patterns is important for ecological and conservation research, and spatially explicit individual-based methods have been recognised as powerful tools in this context. Mammalian carnivores are intrinsically vulnerable to habitat fragmentation but not much is known about the genetic consequences of fragmentation in common species. Stone martens (Martes foina) and red foxes (Vulpes vulpes) share a widespread Palearctic distribution and are considered habitat generalists, but in the Iberian Peninsula stone martens tend to occur in higher quality habitats. We compared their genetic structure in Portugal to see if they are consistent with their differences in ecological plasticity, and also to illustrate an approach to explicitly delineate the spatial boundaries of consistently identified genetic units. We analysed microsatellite data using spatial Bayesian clustering methods (implemented in the software BAPS, GENELAND and TESS), a progressive partitioning approach and a multivariate technique (Spatial Principal Components Analysis-sPCA). Three consensus Bayesian clusters were identified for the stone marten. No consensus was achieved for the red fox, but one cluster was the most probable clustering solution. Progressive partitioning and sPCA suggested additional clusters in the stone marten but they were not consistent among methods and were geographically incoherent. The contrasting results between the two species are consistent with the literature reporting stricter ecological requirements of the stone marten in the Iberian Peninsula. The observed genetic structure in the stone marten may have been influenced by landscape features, particularly rivers, and fragmentation. We suggest that an approach based on a consensus clustering solution of multiple different algorithms may provide an objective and effective means to delineate potential boundaries of inferred subpopulations. sPCA and progressive partitioning offer further verification of possible population structure and may be useful for revealing cryptic spatial genetic patterns worth further investigation. PMID:26727497

Increased dermal collagen bundle alignment in systemic sclerosis is associated with a cell migration signature and role of Arhgdib in directed fibroblast migration on aligned ECMs

PubMed Central

Lafyatis, Robert; Burkly, Linda C.

2017-01-01

Systemic sclerosis (SSc) is a devastating disease affecting the skin and internal organs. Dermal fibrosis manifests early and Modified Rodnan Skin Scores (MRSS) correlate with disease progression. Transcriptomics of SSc skin biopsies suggest the role of the in vivo microenvironment in maintaining the pathological myofibroblasts. Therefore, defining the structural changes in dermal collagen in SSc patients could inform our understanding of fibrosis pathogenesis. Here, we report a method for quantitative whole-slide image analysis of dermal collagen from SSc patients, and our findings of more aligned dermal collagen bundles in diffuse cutaneous SSc (dcSSc) patients. Using the bleomycin-induced mouse model of SSc, we identified a distinct high dermal collagen bundle alignment gene signature, characterized by a concerted upregulation in cell migration, adhesion, and guidance pathways, and downregulation of spindle, replication, and cytokinesis pathways. Furthermore, increased bundle alignment induced a cell migration gene signature in fibroblasts in vitro, and these cells demonstrated increased directed migration on aligned ECM fibers that is dependent on expression of Arhgdib (Rho GDP-dissociation inhibitor 2). Our results indicate that increased cell migration is a cellular response to the increased collagen bundle alignment featured in fibrotic skin. Moreover, many of the cell migration genes identified in our study are shared with human SSc skin and may be new targets for therapeutic intervention. PMID:28662216

Hunter-Gatherer Color Naming Provides New Insight into the Evolution of Color Terms.

PubMed

Lindsey, Delwin T; Brown, Angela M; Brainard, David H; Apicella, Coren L

2015-09-21

Most people name the myriad colors in the environment using between two and about a dozen color terms, with great variation within and between languages. Investigators generally agree that color lexicons evolve from fewer terms to more terms, as technology advances and color communication becomes increasingly important. However, little is understood about the color naming systems at the least technologically advanced end of the continuum. The Hadza people of Tanzania are nomadic hunter-gatherers who live a subsistence lifestyle that was common before the advent of agriculture (see Supplemental Experimental Procedures, section I;), suggesting that the Hadzane language should be at an early stage of color lexicon evolution. When Hadza, Somali, and US informants named 23 color samples, Hadza informants named only the black, white, and red samples with perfect consensus. Otherwise, they used low-consensus terms or responded "don't know." However, even low-consensus color terms grouped test colors into lexical categories that aligned with those found in other world languages. Furthermore, information-theoretic analysis showed that color communication efficiency within the Hadza, Somali, and US language communities falls on the same continuum as other world languages. Thus, the structure of color categories is in place in Hadzane, even though words for many of the categories are not in general use. These results suggest that even very simple color lexicons include precursors of many color categories but that these categories are initially represented in a diverse and distributed fashion. Copyright © 2015 Elsevier Ltd. All rights reserved.

Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis

PubMed Central

Neerincx, Pieter BT; Casel, Pierrot; Prickett, Dennis; Nie, Haisheng; Watson, Michael; Leunissen, Jack AM; Groenen, Martien AM; Klopp, Christophe

2009-01-01

Background Reliable annotation linking oligonucleotide probes to target genes is essential for functional biological analysis of microarray experiments. We used the IMAD, OligoRAP and sigReannot pipelines to update the annotation for the ARK-Genomics Chicken 20 K array as part of a joined EADGENE/SABRE workshop. In this manuscript we compare their annotation strategies and results. Furthermore, we analyse the effect of differences in updated annotation on functional analysis for an experiment involving Eimeria infected chickens and finally we propose guidelines for optimal annotation strategies. Results IMAD, OligoRAP and sigReannot update both annotation and estimated target specificity. The 3 pipelines can assign oligos to target specificity categories although with varying degrees of resolution. Target specificity is judged based on the amount and type of oligo versus target-gene alignments (hits), which are determined by filter thresholds that users can adjust based on their experimental conditions. Linking oligos to annotation on the other hand is based on rigid rules, which differ between pipelines. For 52.7% of the oligos from a subset selected for in depth comparison all pipelines linked to one or more Ensembl genes with consensus on 44.0%. In 31.0% of the cases none of the pipelines could assign an Ensembl gene to an oligo and for the remaining 16.3% the coverage differed between pipelines. Differences in updated annotation were mainly due to different thresholds for hybridisation potential filtering of oligo versus target-gene alignments and different policies for expanding annotation using indirect links. The differences in updated annotation packages had a significant effect on GO term enrichment analysis with consensus on only 67.2% of the enriched terms. Conclusion In addition to flexible thresholds to determine target specificity, annotation tools should provide metadata describing the relationships between oligos and the annotation assigned to them. These relationships can then be used to judge the varying degrees of reliability allowing users to fine-tune the balance between reliability and coverage. This is important as it can have a significant effect on functional microarray analysis as exemplified by the lack of consensus on almost one third of the terms found with GO term enrichment analysis based on updated IMAD, OligoRAP or sigReannot annotation. PMID:19615109

Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis.

PubMed

Neerincx, Pieter Bt; Casel, Pierrot; Prickett, Dennis; Nie, Haisheng; Watson, Michael; Leunissen, Jack Am; Groenen, Martien Am; Klopp, Christophe

2009-07-16

Reliable annotation linking oligonucleotide probes to target genes is essential for functional biological analysis of microarray experiments. We used the IMAD, OligoRAP and sigReannot pipelines to update the annotation for the ARK-Genomics Chicken 20 K array as part of a joined EADGENE/SABRE workshop. In this manuscript we compare their annotation strategies and results. Furthermore, we analyse the effect of differences in updated annotation on functional analysis for an experiment involving Eimeria infected chickens and finally we propose guidelines for optimal annotation strategies. IMAD, OligoRAP and sigReannot update both annotation and estimated target specificity. The 3 pipelines can assign oligos to target specificity categories although with varying degrees of resolution. Target specificity is judged based on the amount and type of oligo versus target-gene alignments (hits), which are determined by filter thresholds that users can adjust based on their experimental conditions. Linking oligos to annotation on the other hand is based on rigid rules, which differ between pipelines.For 52.7% of the oligos from a subset selected for in depth comparison all pipelines linked to one or more Ensembl genes with consensus on 44.0%. In 31.0% of the cases none of the pipelines could assign an Ensembl gene to an oligo and for the remaining 16.3% the coverage differed between pipelines. Differences in updated annotation were mainly due to different thresholds for hybridisation potential filtering of oligo versus target-gene alignments and different policies for expanding annotation using indirect links. The differences in updated annotation packages had a significant effect on GO term enrichment analysis with consensus on only 67.2% of the enriched terms. In addition to flexible thresholds to determine target specificity, annotation tools should provide metadata describing the relationships between oligos and the annotation assigned to them. These relationships can then be used to judge the varying degrees of reliability allowing users to fine-tune the balance between reliability and coverage. This is important as it can have a significant effect on functional microarray analysis as exemplified by the lack of consensus on almost one third of the terms found with GO term enrichment analysis based on updated IMAD, OligoRAP or sigReannot annotation.

[Identification of Tibetan medicine "Dida" of Gentianaceae using DNA barcoding].

PubMed

Liu, Chuan; Zhang, Yu-Xin; Liu, Yue; Chen, Yi-Long; Fan, Gang; Xiang, Li; Xu, Jiang; Zhang, Yi

2016-02-01

The ITS2 barcode was used toidentify Tibetan medicine "Dida", and tosecure its quality and safety in medication. A total of 13 species, 151 experimental samples for the study from the Tibetan Plateau, including Gentianaceae Swertia, Halenia, Gentianopsis, Comastoma, Lomatogonium ITS2 sequences were amplified, and purified PCR products were sequenced. Sequence assembly and consensus sequence generation were performed using the CodonCode Aligner V3.7.1. The Kimura 2-Parameter (K2P) distances were calculated using MEGA 6.0. The neighbor-joining (NJ) phylogenetic trees were constructed. There are 31 haplotypes among 231 bp after alignment of all ITS2 sequence haplotypes, and the average G±C content of 61.40%. The NJ tree strongly supported that every species clustered into their own clade and high identification success rate, except that Swertia bifolia and Swertia wolfangiana could not be distinguished from each other based on the sequence divergences. DNA barcoding could be used as a fast and accurate identification method to distinguish Tibetan medicine "Dida" to ensure its safe use. Copyright© by the Chinese Pharmaceutical Association.

Describing sequencing results of structural chromosome rearrangements with a suggested next-generation cytogenetic nomenclature.

PubMed

Ordulu, Zehra; Wong, Kristen E; Currall, Benjamin B; Ivanov, Andrew R; Pereira, Shahrin; Althari, Sara; Gusella, James F; Talkowski, Michael E; Morton, Cynthia C

2014-05-01

With recent rapid advances in genomic technologies, precise delineation of structural chromosome rearrangements at the nucleotide level is becoming increasingly feasible. In this era of "next-generation cytogenetics" (i.e., an integration of traditional cytogenetic techniques and next-generation sequencing), a consensus nomenclature is essential for accurate communication and data sharing. Currently, nomenclature for describing the sequencing data of these aberrations is lacking. Herein, we present a system called Next-Gen Cytogenetic Nomenclature, which is concordant with the International System for Human Cytogenetic Nomenclature (2013). This system starts with the alignment of rearrangement sequences by BLAT or BLAST (alignment tools) and arrives at a concise and detailed description of chromosomal changes. To facilitate usage and implementation of this nomenclature, we are developing a program designated BLA(S)T Output Sequence Tool of Nomenclature (BOSToN), a demonstrative version of which is accessible online. A standardized characterization of structural chromosomal rearrangements is essential both for research analyses and for application in the clinical setting. Copyright © 2014 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Unsupervised consensus cluster analysis of [18F]-fluoroethyl-L-tyrosine positron emission tomography identified textural features for the diagnosis of pseudoprogression in high-grade glioma.

PubMed

Kebir, Sied; Khurshid, Zain; Gaertner, Florian C; Essler, Markus; Hattingen, Elke; Fimmers, Rolf; Scheffler, Björn; Herrlinger, Ulrich; Bundschuh, Ralph A; Glas, Martin

2017-01-31

Timely detection of pseudoprogression (PSP) is crucial for the management of patients with high-grade glioma (HGG) but remains difficult. Textural features of O-(2-[18F]fluoroethyl)-L-tyrosine positron emission tomography (FET-PET) mirror tumor uptake heterogeneity; some of them may be associated with tumor progression. Fourteen patients with HGG and suspected of PSP underwent FET-PET imaging. A set of 19 conventional and textural FET-PET features were evaluated and subjected to unsupervised consensus clustering. The final diagnosis of true progression vs. PSP was based on follow-up MRI using RANO criteria. Three robust clusters have been identified based on 10 predominantly textural FET-PET features. None of the patients with PSP fell into cluster 2, which was associated with high values for textural FET-PET markers of uptake heterogeneity. Three out of 4 patients with PSP were assigned to cluster 3 that was largely associated with low values of textural FET-PET features. By comparison, tumor-to-normal brain ratio (TNRmax) at the optimal cutoff 2.1 was less predictive of PSP (negative predictive value 57% for detecting true progression, p=0.07 vs. 75% with cluster 3, p=0.04). Clustering based on textural O-(2-[18F]fluoroethyl)-L-tyrosine PET features may provide valuable information in assessing the elusive phenomenon of pseudoprogression.

Spinal alignment in surgical, multisegmental, transpedicular correction of adolescent idiopathic scoliosis

PubMed Central

Nowakowski, Andrzej; Dworak, Lechosław B.; Kubaszewski, Łukasz; Kaczmarczyk, Jacek

2012-01-01

Summary The objective of this study was to discuss the variables influencing alignment mechanisms of the spine, with particular consideration of post-surgical alignment in adolescent idiopathic scoliosis. The analysis is based on information currently available in the literature, and on the authors’ own experience, which includes surgical material from over 2200 cases of idiopathic scoliosis. Over 50% of cases of adolescent idiopathic scoliosis are decompensated before surgical treatment. Spinal alignment is most significantly influenced by the position of the pelvis. Surgical restoration of lumbar lordosis is more important than attempting to restore thoracic kyphosis in the sagittal plane. The sagittal profile has an essential impact on spinal alignment. The same curves in the coronal plane can have various 3-dimensional configurations. Clinical difficulties in the assessment of thoracic kyphosis and lumbar lordosis result from the fact that they undergo constant change with age. Thoracic hypokyphosis diagnosed before surgery is a very frequent symptom of curve progression. The presence of proximal (thoraco-thoracic) and distal (thoraco-lumbar) junctional kyphosis is very important for planning the scope of spondylodesis. The natural tendency of the spine for alignment (compensation) after surgery nowadays occurs more naturally by applying derotational forces through pedicle screws, compared to the distraction devices (eg, Harrington rod) used in the past. PMID:23229319

Rapid Transfer Alignment of MEMS SINS Based on Adaptive Incremental Kalman Filter.

PubMed

Chu, Hairong; Sun, Tingting; Zhang, Baiqiang; Zhang, Hongwei; Chen, Yang

2017-01-14

In airborne MEMS SINS transfer alignment, the error of MEMS IMU is highly environment-dependent and the parameters of the system model are also uncertain, which may lead to large error and bad convergence of the Kalman filter. In order to solve this problem, an improved adaptive incremental Kalman filter (AIKF) algorithm is proposed. First, the model of SINS transfer alignment is defined based on the "Velocity and Attitude" matching method. Then the detailed algorithm progress of AIKF and its recurrence formulas are presented. The performance and calculation amount of AKF and AIKF are also compared. Finally, a simulation test is designed to verify the accuracy and the rapidity of the AIKF algorithm by comparing it with KF and AKF. The results show that the AIKF algorithm has better estimation accuracy and shorter convergence time, especially for the bias of the gyroscope and the accelerometer, which can meet the accuracy and rapidity requirement of transfer alignment.

Rapid Transfer Alignment of MEMS SINS Based on Adaptive Incremental Kalman Filter

PubMed Central

Chu, Hairong; Sun, Tingting; Zhang, Baiqiang; Zhang, Hongwei; Chen, Yang

2017-01-01

In airborne MEMS SINS transfer alignment, the error of MEMS IMU is highly environment-dependent and the parameters of the system model are also uncertain, which may lead to large error and bad convergence of the Kalman filter. In order to solve this problem, an improved adaptive incremental Kalman filter (AIKF) algorithm is proposed. First, the model of SINS transfer alignment is defined based on the “Velocity and Attitude” matching method. Then the detailed algorithm progress of AIKF and its recurrence formulas are presented. The performance and calculation amount of AKF and AIKF are also compared. Finally, a simulation test is designed to verify the accuracy and the rapidity of the AIKF algorithm by comparing it with KF and AKF. The results show that the AIKF algorithm has better estimation accuracy and shorter convergence time, especially for the bias of the gyroscope and the accelerometer, which can meet the accuracy and rapidity requirement of transfer alignment. PMID:28098829

Building up the spin - orbit alignment of interacting galaxy pairs

NASA Astrophysics Data System (ADS)

Moon, Jun-Sung; Yoon, Suk-Jin

2018-01-01

Galaxies are not just randomly distributed throughout space. Instead, they are in alignment over a wide range of scales from the cosmic web down to a pair of galaxies. Motivated by recent findings that the spin and the orbital angular momentum vectors of galaxy pairs tend to be parallel, we here investigate the spin - orbit orientation in close pairs using the Illustris cosmological simulation. We find that since z ~ 1, the parallel alignment has become progressively stronger with time through repetitive encounters. The pair Interactions are preferentially in prograde at z = 0 (over 5 sigma significance). The prograde fraction at z = 0 is larger for the pairs influenced more heavily by each other during their evolution. We find no correlation between the spin - orbit orientation and the surrounding large-scale structure. Our results favor the scenario in which the alignment in close pairs is caused by tidal interactions later on, rather than the primordial torquing by the large-scale structures.

An efficient multi-resolution GA approach to dental image alignment

NASA Astrophysics Data System (ADS)

Nassar, Diaa Eldin; Ogirala, Mythili; Adjeroh, Donald; Ammar, Hany

2006-02-01

Automating the process of postmortem identification of individuals using dental records is receiving an increased attention in forensic science, especially with the large volume of victims encountered in mass disasters. Dental radiograph alignment is a key step required for automating the dental identification process. In this paper, we address the problem of dental radiograph alignment using a Multi-Resolution Genetic Algorithm (MR-GA) approach. We use location and orientation information of edge points as features; we assume that affine transformations suffice to restore geometric discrepancies between two images of a tooth, we efficiently search the 6D space of affine parameters using GA progressively across multi-resolution image versions, and we use a Hausdorff distance measure to compute the similarity between a reference tooth and a query tooth subject to a possible alignment transform. Testing results based on 52 teeth-pair images suggest that our algorithm converges to reasonable solutions in more than 85% of the test cases, with most of the error in the remaining cases due to excessive misalignments.

Office of Biological and Physical Research: Overview Transitioning to the Vision for Space Exploration

NASA Technical Reports Server (NTRS)

Crouch, Roger

2004-01-01

Viewgraphs on NASA's transition to its vision for space exploration is presented. The topics include: 1) Strategic Directives Guiding the Human Support Technology Program; 2) Progressive Capabilities; 3) A Journey to Inspire, Innovate, and Discover; 4) Risk Mitigation Status Technology Readiness Level (TRL) and Countermeasures Readiness Level (CRL); 5) Biological And Physical Research Enterprise Aligning With The Vision For U.S. Space Exploration; 6) Critical Path Roadmap Reference Missions; 7) Rating Risks; 8) Current Critical Path Roadmap (Draft) Rating Risks: Human Health; 9) Current Critical Path Roadmap (Draft) Rating Risks: System Performance/Efficiency; 10) Biological And Physical Research Enterprise Efforts to Align With Vision For U.S. Space Exploration; 11) Aligning with the Vision: Exploration Research Areas of Emphasis; 12) Code U Efforts To Align With The Vision For U.S. Space Exploration; 13) Types of Critical Path Roadmap Risks; and 14) ISS Human Support Systems Research, Development, and Demonstration. A summary discussing the vision for U.S. space exploration is also provided.

StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase.

PubMed

Zemla, Adam T; Lang, Dorothy M; Kostova, Tanya; Andino, Raul; Ecale Zhou, Carol L

2011-06-02

Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more satisfactory--still, they cannot provide reliable results at low levels of sequence identity. Our goal in the current work was to develop an algorithm that could help overcome these difficulties by facilitating the identification of structurally (and possibly functionally) relevant residue-residue correspondences between compared protein structures. Here we present StralSV (structure-alignment sequence variability), a new algorithm for detecting closely related structure fragments and quantifying residue frequency from tight local structure alignments. We apply StralSV in a study of the RNA-dependent RNA polymerase of poliovirus, and we demonstrate that the algorithm can be used to determine regions of the protein that are relatively unique, or that share structural similarity with proteins that would be considered distantly related. By quantifying residue frequencies among many residue-residue pairs extracted from local structural alignments, one can infer potential structural or functional importance of specific residues that are determined to be highly conserved or that deviate from a consensus. We further demonstrate that considerable detailed structural and phylogenetic information can be derived from StralSV analyses. StralSV is a new structure-based algorithm for identifying and aligning structure fragments that have similarity to a reference protein. StralSV analysis can be used to quantify residue-residue correspondences and identify residues that may be of particular structural or functional importance, as well as unusual or unexpected residues at a given sequence position. StralSV is provided as a web service at http://proteinmodel.org/AS2TS/STRALSV/.

Making Basic Science Studies in Glaucoma More Clinically Relevant: The Need for a Consensus.

PubMed

Toris, Carol B; Gelfman, Claire; Whitlock, Andy; Sponsel, William E; Rowe-Rendleman, Cheryl L

2017-09-01

Glaucoma is a chronic, progressive, and debilitating optic neuropathy that causes retinal damage and visual defects. The pathophysiologic mechanisms of glaucoma remain ill-defined, and there is an indisputable need for contributions from basic science researchers in defining pathways for translational research. However, glaucoma researchers today face significant challenges due to the lack of a map of integrated pathways from bench to bedside and the lack of consensus statements to guide in choosing the right research questions, techniques, and model systems. Here, we present the case for the development of such maps and consensus statements, which are critical for faster development of the most efficacious glaucoma therapy. We underscore that interrogating the preclinical path of both successful and unsuccessful clinical programs is essential to defining future research. One aspect of this is evaluation of available preclinical research tools. To begin this process, we highlight the utility of currently available animal models for glaucoma and emphasize that there is a particular need for models of glaucoma with normal intraocular pressure. In addition, we outline a series of discoveries from cell-based, animal, and translational research that begin to reveal a map of glaucoma from cell biology to physiology to disease pathology. Completion of these maps requires input and consensus from the global glaucoma research community. This article sets the stage by outlining various approaches to such a consensus. Together, these efforts will help accelerate basic science research, leading to discoveries with significant clinical impact for people with glaucoma.

Health promotion competencies: providing a road map for health promotion to assume a prominent role in global health.

PubMed

Shilton, Trevor

2009-06-01

Understanding of health and its determinants is rapidly expanding and changing. The emergence of chronic diseases as the leading cause of global disease burden and improved understanding of social determinants of health has brought greater focus to the role of prevention in health. The IUHPE has shown outstanding leadership through the Galway Consensus Statement. Its three recommendations appropriately focus on stimulating dialogue, developing global consensus and communicating the results to key stakeholders. The IUHPE can further enhance progress of the statement by developing participative processes to ensure engagement and ownership by its members. The Galway Consensus Statement can be used to advance professional standards in global health promotion by: (1) providing a common language by which health promotion and its meaning can be communicated to others; (2) providing a framework for building capacity in the health promotion workforce and in the health workforce in general; (3) providing international consensus for consistency in university health promotion courses; (4) providing a framework for credentialing in health promotion; (5) better informing health promotion engagement with other significant workforce sectors and advancing partnership as a key way of working. A vital further application of the Galway Consensus Statement is to inform advocacy. Advocacy is vital to ensure health promotion is better resourced and prioritized by policy makers. Advocacy and communication are vital tools to highlight the evidence, establish the policy fit and infrastructure requirements of health promotion, and present health promotion solutions based on evidence of effectiveness.

Tuberous sclerosis complex surveillance and management: recommendations of the 2012 International Tuberous Sclerosis Complex Consensus Conference.

PubMed

Krueger, Darcy A; Northrup, Hope

2013-10-01

Tuberous sclerosis complex is a genetic disorder affecting every organ system, but disease manifestations vary significantly among affected individuals. The diverse and varied presentations and progression can be life-threatening with significant impact on cost and quality of life. Current surveillance and management practices are highly variable among region and country, reflective of the fact that last consensus recommendations occurred in 1998 and an updated, comprehensive standard is lacking that incorporates the latest scientific evidence and current best clinical practices. The 2012 International Tuberous Sclerosis Complex Consensus Group, comprising 79 specialists from 14 countries, was organized into 12 separate subcommittees, each led by a clinician with advanced expertise in tuberous sclerosis complex and the relevant medical subspecialty. Each subcommittee focused on a specific disease area with important clinical management implications and was charged with formulating key clinical questions to address within its focus area, reviewing relevant literature, evaluating the strength of data, and providing a recommendation accordingly. The updated consensus recommendations for clinical surveillance and management in tuberous sclerosis complex are summarized here. The recommendations are relevant to the entire lifespan of the patient, from infancy to adulthood, including both individuals where the diagnosis is newly made as well as individuals where the diagnosis already is established. The 2012 International Tuberous Sclerosis Complex Consensus Recommendations provide an evidence-based, standardized approach for optimal clinical care provided for individuals with tuberous sclerosis complex. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Dynamic localization of Mps1 kinase to kinetochores is essential for accurate spindle microtubule attachment

PubMed Central

Dou, Zhen; Liu, Xing; Wang, Wenwen; Zhu, Tongge; Wang, Xinghui; Xu, Leilei; Abrieu, Ariane; Fu, Chuanhai; Hill, Donald L.; Yao, Xuebiao

2015-01-01

The spindle assembly checkpoint (SAC) is a conserved signaling pathway that monitors faithful chromosome segregation during mitosis. As a core component of SAC, the evolutionarily conserved kinase monopolar spindle 1 (Mps1) has been implicated in regulating chromosome alignment, but the underlying molecular mechanism remains unclear. Our molecular delineation of Mps1 activity in SAC led to discovery of a previously unidentified structural determinant underlying Mps1 function at the kinetochores. Here, we show that Mps1 contains an internal region for kinetochore localization (IRK) adjacent to the tetratricopeptide repeat domain. Importantly, the IRK region determines the kinetochore localization of inactive Mps1, and an accumulation of inactive Mps1 perturbs accurate chromosome alignment and mitotic progression. Mechanistically, the IRK region binds to the nuclear division cycle 80 complex (Ndc80C), and accumulation of inactive Mps1 at the kinetochores prevents a dynamic interaction between Ndc80C and spindle microtubules (MTs), resulting in an aberrant kinetochore attachment. Thus, our results present a previously undefined mechanism by which Mps1 functions in chromosome alignment by orchestrating Ndc80C–MT interactions and highlight the importance of the precise spatiotemporal regulation of Mps1 kinase activity and kinetochore localization in accurate mitotic progression. PMID:26240331

Dynamic localization of Mps1 kinase to kinetochores is essential for accurate spindle microtubule attachment.

PubMed

Dou, Zhen; Liu, Xing; Wang, Wenwen; Zhu, Tongge; Wang, Xinghui; Xu, Leilei; Abrieu, Ariane; Fu, Chuanhai; Hill, Donald L; Yao, Xuebiao

2015-08-18

The spindle assembly checkpoint (SAC) is a conserved signaling pathway that monitors faithful chromosome segregation during mitosis. As a core component of SAC, the evolutionarily conserved kinase monopolar spindle 1 (Mps1) has been implicated in regulating chromosome alignment, but the underlying molecular mechanism remains unclear. Our molecular delineation of Mps1 activity in SAC led to discovery of a previously unidentified structural determinant underlying Mps1 function at the kinetochores. Here, we show that Mps1 contains an internal region for kinetochore localization (IRK) adjacent to the tetratricopeptide repeat domain. Importantly, the IRK region determines the kinetochore localization of inactive Mps1, and an accumulation of inactive Mps1 perturbs accurate chromosome alignment and mitotic progression. Mechanistically, the IRK region binds to the nuclear division cycle 80 complex (Ndc80C), and accumulation of inactive Mps1 at the kinetochores prevents a dynamic interaction between Ndc80C and spindle microtubules (MTs), resulting in an aberrant kinetochore attachment. Thus, our results present a previously undefined mechanism by which Mps1 functions in chromosome alignment by orchestrating Ndc80C-MT interactions and highlight the importance of the precise spatiotemporal regulation of Mps1 kinase activity and kinetochore localization in accurate mitotic progression.

Cages of Their Own Design: Five Strategies to Help Education Leaders Break Free. Education Outlook No. 1

ERIC Educational Resources Information Center

Hess, Frederick M.

2010-01-01

The education profession is notorious for its resistance to change. School leaders often claim that collective bargaining agreements, state and federal regulations, and budget concerns prevent them from pursuing effective school reform. The culture of the K-12 leadership environment is one that often seeks consensus over progress and collegiality…

Assessment Update: Progress, Trends, and Practices in Higher Education. Volume 26, Issue 2, March-April 2014

ERIC Educational Resources Information Center

Banta, Trudy W., Ed.

2014-01-01

This issue of "Assessment Update" presents the following articles: (1) Effective Leadership Assessment: A 360-Degree Process; (2) Editor's Notes: Accentuating the Positive in Our Work; (3) The Broadcast Education Association's Model Rubrics Project: Building Consensus One Rubric at a Time; (4) Building a Better…

First Brazilian Consensus of Advanced Prostate Cancer: Recommendations for Clinical Practice.

PubMed

Sasse, Andre Deeke; Wiermann, Evanius Garcia; Herchenhorn, Daniel; Bastos, Diogo Assed; Schutz, Fabio A; Maluf, Fernando Cotait; Coura, George; Morbeck, Igor Alexandre Protzner; Cerci, Juliano J; Smaletz, Oren; Lima, Volney Soares; Adamy, Ari; Campos, Franz Santos de; Carvalhal, Gustavo Franco; Cezar, Leandro Casemiro; Dall'Oglio, Marcos Francisco; Sadi, Marcus Vinicius; Reis, Rodolfo Borges Dos; Nogueira, Lucas

2017-01-01

Prostate cancer still represents a major cause of morbidity, and still about 20% of men with the disease are diagnosed or will progress to the advanced stage without the possibility of curative treatment. Despite the recent advances in scientific and technological knowledge and the availability of new therapies, there is still considerable heterogeneity in the therapeutic approaches for metastatic prostate cancer. This article presents a summary of the I Brazilian Consensus on Advanced Prostate Cancer, conducted by the Brazilian Society of Urology and Brazilian Society of Clinical Oncology. Experts were selected by the medical societies involved. Forty issues regarding controversial issues in advanced disease were previously elaborated. The panel met for consensus, with a threshold established for 2/3 of the participants. The treatment of advanced prostate cancer is complex, due to the existence of a large number of therapies, with different response profiles and toxicities. The panel addressed recommendations on preferred choice of therapies, indicators that would justify their change, and indicated some strategies for better sequencing of treatment in order to maximize the potential for disease control with the available therapeutic arsenal. The lack of consensus on some topics clearly indicates the absence of strong evidence for some decisions. Copyright® by the International Brazilian Journal of Urology.

Too Fit To Fracture: outcomes of a Delphi consensus process on physical activity and exercise recommendations for adults with osteoporosis with or without vertebral fractures.

PubMed

Giangregorio, L M; McGill, S; Wark, J D; Laprade, J; Heinonen, A; Ashe, M C; MacIntyre, N J; Cheung, A M; Shipp, K; Keller, H; Jain, R; Papaioannou, A

2015-03-01

An international consensus process resulted in exercise and physical activity recommendations for individuals with osteoporosis. Emphasis was placed on strength, balance, and postural alignment. Rather than providing generic restrictions, activity should be encouraged while considering impairments, fracture risk, activity history, and preference, and guidance on spine sparing techniques should be provided. The objectives of this study were to establish expert consensus on key questions posed by patients or health care providers regarding recommended assessment domains to inform exercise prescription, therapeutic goals of exercise, and physical activity and exercise recommendations for individuals with osteoporosis or osteoporotic vertebral fracture. The Too Fit To Fracture expert panel identified researchers and clinicians with expertise in exercise and osteoporosis and stakeholder groups. We delivered a modified online Delphi survey (two rounds) to establish consensus on assessment, exercise, and physical activities for three cases with varying risk (osteoporosis based on bone mineral density; 1 spine fracture and osteoporosis; multiple spine fractures, osteoporosis, hyperkyphosis, and pain). Duplicate content analyses of free text responses were performed. Response rates were 52% (39/75) and 69% (48/70) for each round. Key consensus points are the following: (a) Current physical activity guidelines are appropriate for individuals with osteoporosis without spine fracture, but not for those with spine fracture; (b) after spine fracture, physical activity of moderate intensity is preferred to vigorous; (c) daily balance training and endurance training for spinal extensor muscles are recommended for all; (d) providing guidance on spine-sparing techniques (e.g., hip hinge) during activities of daily living or leisure, considering impairments, fracture risk, activity history, and preference, is recommended rather than providing generic restrictions (e.g., lifting <10 lbs, no twisting), but for those with vertebral fracture, especially in the presence of pain, multiple fractures, or hyperkyphosis, the risks of many activities may outweigh the benefits-physical therapist consultation is recommended. Examples of spine-sparing techniques and exercise prescription elements are provided. Our recommendations guide health care providers on assessment, exercise prescription, and safe movement for individuals with osteoporosis.

Too Fit To Fracture: outcomes of a Delphi consensus process on physical activity and exercise recommendations for adults with osteoporosis with or without vertebral fractures

PubMed Central

McGill, S.; Wark, J. D.; Laprade, J.; Heinonen, A.; Ashe, M. C.; MacIntyre, N. J.; Cheung, A. M.; Shipp, K.; Keller, H.; Jain, R.; Papaioannou, A.

2016-01-01

Summary An international consensus process resulted in exercise and physical activity recommendations for individuals with osteoporosis. Emphasis was placed on strength, balance, and postural alignment. Rather than providing generic restrictions, activity should be encouraged while considering impairments, fracture risk, activity history, and preference, and guidance on spine sparing techniques should be provided. Introduction The objectives of this study were to establish expert consensus on key questions posed by patients or health care providers regarding recommended assessment domains to inform exercise prescription, therapeutic goals of exercise, and physical activity and exercise recommendations for individuals with osteoporosis or osteoporotic vertebral fracture. Methods The Too Fit To Fracture expert panel identified researchers and clinicians with expertise in exercise and osteoporosis and stakeholder groups. We delivered a modified online Delphi survey (two rounds) to establish consensus on assessment, exercise, and physical activities for three cases with varying risk (osteoporosis based on bone mineral density; 1 spine fracture and osteoporosis; multiple spine fractures, osteoporosis, hyperkyphosis, and pain). Duplicate content analyses of free text responses were performed. Results Response rates were 52 % (39/75) and 69 % (48/70) for each round. Key consensus points are the following: (a) Current physical activity guidelines are appropriate for individuals with osteoporosis without spine fracture, but not for those with spine fracture; (b) after spine fracture, physical activity of moderate intensity is preferred to vigorous; (c) daily balance training and endurance training for spinal extensor muscles are recommended for all; (d) providing guidance on spine-sparing techniques (e.g., hip hinge) during activities of daily living or leisure, considering impairments, fracture risk, activity history, and preference, is recommended rather than providing generic restrictions (e.g., lifting <10 lbs, no twisting), but for those with vertebral fracture, especially in the presence of pain, multiple fractures, or hyperkyphosis, the risks of many activities may outweigh the benefits—physical therapist consultation is recommended. Examples of spine-sparing techniques and exercise prescription elements are provided. Conclusions Our recommendations guide health care providers on assessment, exercise prescription, and safe movement for individuals with osteoporosis. PMID:25510579

International consensus statements on early chronic Pancreatitis. Recommendations from the working group for the international consensus guidelines for chronic pancreatitis in collaboration with The International Association of Pancreatology, American Pancreatic Association, Japan Pancreas Society, PancreasFest Working Group and European Pancreatic Club.

PubMed

Whitcomb, David C; Shimosegawa, Tooru; Chari, Suresh T; Forsmark, Christopher E; Frulloni, Luca; Garg, Pramod; Hegyi, Peter; Hirooka, Yoshiki; Irisawa, Atsushi; Ishikawa, Takuya; Isaji, Shuiji; Lerch, Markus M; Levy, Philippe; Masamune, Atsushi; Wilcox, Charles M; Windsor, John; Yadav, Dhiraj; Sheel, Andrea; Neoptolemos, John P

2018-05-21

Chronic pancreatitis (CP) is a progressive inflammatory disorder currently diagnosed by morphologic features. In contrast, an accurate diagnosis of Early CP is not possible using imaging criteria alone. If this were possible and early treatment instituted, the later, irreversible features and complications of CP could possibly be prevented. An international working group supported by four major pancreas societies (IAP, APA, JPS, and EPC) and a PancreasFest working group sought to develop a consensus definition and diagnostic criteria for Early CP. Ten statements (S1-10) concerning Early CP were used to gauge consensus on the Early CP concept using anonymous voting with a 9 point Likert scale. Consensus required an alpha ≥0.80. No consensus statement could be developed for a definition of Early-CP or diagnostic criteria. There was consensus on 5 statements: (S2) The word "Early" in early chronic pancreatitis is used to describe disease state, not disease duration. (S4) Early CP defines a stage of CP with preserved pancreatic function and potentially reversible features. (S8) Genetic variants are important risk factors for Early CP and can add specificity to the likely etiology, but they are neither necessary nor sufficient to make a diagnosis. (S9) Environmental risk factors can provide evidence to support the diagnosis of Early CP, but are neither necessary nor sufficient to make a diagnosis. (S10) The differential diagnosis for Early CP includes other disorders with morphological and functional features that overlap with CP. Morphology based diagnosis of Early CP is not possible without additional information. New approaches to the accurate diagnosis of Early CP will require a mechanistic definition that considers risk factors, biomarkers, clinical context and new models of disease. Such a definition will require prospective validation. Copyright © 2018. Published by Elsevier B.V.

Computer Vision Evidence Supporting Craniometric Alignment of Rat Brain Atlases to Streamline Expert-Guided, First-Order Migration of Hypothalamic Spatial Datasets Related to Behavioral Control

PubMed Central

Khan, Arshad M.; Perez, Jose G.; Wells, Claire E.; Fuentes, Olac

2018-01-01

The rat has arguably the most widely studied brain among all animals, with numerous reference atlases for rat brain having been published since 1946. For example, many neuroscientists have used the atlases of Paxinos and Watson (PW, first published in 1982) or Swanson (S, first published in 1992) as guides to probe or map specific rat brain structures and their connections. Despite nearly three decades of contemporaneous publication, no independent attempt has been made to establish a basic framework that allows data mapped in PW to be placed in register with S, or vice versa. Such data migration would allow scientists to accurately contextualize neuroanatomical data mapped exclusively in only one atlas with data mapped in the other. Here, we provide a tool that allows levels from any of the seven published editions of atlases comprising three distinct PW reference spaces to be aligned to atlas levels from any of the four published editions representing S reference space. This alignment is based on registration of the anteroposterior stereotaxic coordinate (z) measured from the skull landmark, Bregma (β). Atlas level alignments performed along the z axis using one-dimensional Cleveland dot plots were in general agreement with alignments obtained independently using a custom-made computer vision application that utilized the scale-invariant feature transform (SIFT) and Random Sample Consensus (RANSAC) operation to compare regions of interest in photomicrographs of Nissl-stained tissue sections from the PW and S reference spaces. We show that z-aligned point source data (unpublished hypothalamic microinjection sites) can be migrated from PW to S space to a first-order approximation in the mediolateral and dorsoventral dimensions using anisotropic scaling of the vector-formatted atlas templates, together with expert-guided relocation of obvious outliers in the migrated datasets. The migrated data can be contextualized with other datasets mapped in S space, including neuronal cell bodies, axons, and chemoarchitecture; to generate data-constrained hypotheses difficult to formulate otherwise. The alignment strategies provided in this study constitute a basic starting point for first-order, user-guided data migration between PW and S reference spaces along three dimensions that is potentially extensible to other spatial reference systems for the rat brain. PMID:29765309

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters.

PubMed

Sela, Itamar; Ashkenazy, Haim; Katoh, Kazutaka; Pupko, Tal

2015-07-01

Inference of multiple sequence alignments (MSAs) is a critical part of phylogenetic and comparative genomics studies. However, from the same set of sequences different MSAs are often inferred, depending on the methodologies used and the assumed parameters. Much effort has recently been devoted to improving the ability to identify unreliable alignment regions. Detecting such unreliable regions was previously shown to be important for downstream analyses relying on MSAs, such as the detection of positive selection. Here we developed GUIDANCE2, a new integrative methodology that accounts for: (i) uncertainty in the process of indel formation, (ii) uncertainty in the assumed guide tree and (iii) co-optimal solutions in the pairwise alignments, used as building blocks in progressive alignment algorithms. We compared GUIDANCE2 with seven methodologies to detect unreliable MSA regions using extensive simulations and empirical benchmarks. We show that GUIDANCE2 outperforms all previously developed methodologies. Furthermore, GUIDANCE2 also provides a set of alternative MSAs which can be useful for downstream analyses. The novel algorithm is implemented as a web-server, available at: http://guidance.tau.ac.il. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Consensus statement with recommendations on active surveillance inclusion criteria and definition of progression in men with localized prostate cancer: the critical role of the pathologist.

PubMed

Montironi, Rodolfo; Hammond, Elizabeth H; Lin, Daniel W; Gore, John L; Srigley, John R; Samaratunga, Hema; Egevad, Lars; Rubin, Mark A; Nacey, John; Klotz, Laurence; Sandler, Howard; Zietman, Anthony L; Holden, Stuart; Humphrey, Peter A; Evans, Andrew J; Delahunt, Brett; McKenney, Jesse K; Berney, Daniel; Wheeler, Thomas M; Chinnaiyan, Arul; True, Lawrence; Knudsen, Beatrice; Epstein, Jonathan I; Amin, Mahul B

2014-12-01

Active surveillance (AS) is an important management option for men with low-risk, clinically localized prostate cancer. The clinical parameters for patient selection and definition of progression for AS protocols are evolving as data from several large cohorts matures. Vital to this process is the critical role pathologic parameters play in identifying appropriate candidates for AS. These findings need to be reproducible and consistently reported by surgical pathologists. This report highlights the importance of accurate pathology reporting as a critical component of these protocols.

Health information technology: strategic initiatives, real progress.

PubMed

Kolodner, Robert M; Cohn, Simon P; Friedman, Charles P

2008-01-01

We fully agree with Carol Diamond and Clay Shirky that deployment of health information technology (IT) is necessary but not sufficient for transforming U.S. health care. However, the recent work to advance health IT is far from an exercise in "magical thinking." It has been strategic thinking. To illustrate this, we highlight recent initiatives and progress under four focus areas: adoption, governance, privacy and security, and interoperability. In addition, solutions exist for health IT to advance rapidly without adversely affecting future policy choices. A broad national consensus is emerging in support of advancing health IT to enable the transformation of health and care.

A Multicenter Radiographic Evaluation of the Rates of Preoperative and Postoperative Malalignment in Degenerative Spinal Fusions.

PubMed

Leveque, Jean-Christophe A; Segebarth, Bradley; Schroerlucke, Samuel R; Khanna, Nitin; Pollina, John; Youssef, Jim A; Tohmeh, Antoine G; Uribe, Juan S

2018-07-01

Multicenter, retrospective, institutional-review-board -approved study at 18 institutions in the United States with 24 treating investigators. This study was designed to retrospectively assess the prevalence of spinopelvic malalignment in patients who underwent one- or two-level lumbar fusions for degenerative (nondeformity) indications and to assess the incidence of malalignment after fusion surgery as well as the rate of alignment preservation and/or correction in this population. Spinopelvic malalignment after lumbar fusion has been associated with lower postoperative health-related quality of life and elevated risk of adjacent segment failure. The prevalence of spinopelvic malalignment in short-segment degenerative lumbar fusion procedures from a large sample of patients is heretofore unreported and may lead to an under-appreciation of these factors in surgical planning and ultimate preservation or correction of alignment. Lateral preoperative and postoperative lumbar radiographs were retrospectively acquired from 578 one- or two-level lumbar fusion patients and newly measured for lumbar lordosis (LL), pelvic incidence (PI), and pelvic tilt. Patients were categorized at preop and postop time points as aligned if PI-LL < 10° or malaligned if PI-LL≥10°. Patients were grouped into categories based on their alignment progression from pre- to postoperative, with preserved (aligned to aligned), restored (malaligned to aligned), not corrected (malaligned to malaligned), and worsened (aligned to malaligned) designations. Preoperatively, 173 (30%) patients exhibited malalignment. Postoperatively, 161 (28%) of patients were malaligned. Alignment was preserved in 63%, restored in 9%, not corrected in 21%, and worsened in 7% of patients. This is the first multicenter study to evaluate the preoperative prevalence and postoperative incidence of spinopelvic malalignment in a large series of short-segment degenerative lumbar fusions, finding over 25% of patients out of alignment at both time points, suggesting that alignment preservation/restoration considerations should be incorporated into the decision-making of even degenerative lumbar spinal fusions. 3.

Forces and moments generated by removable thermoplastic aligners: incisor torque, premolar derotation, and molar distalization.

PubMed

Simon, Mareike; Keilig, Ludger; Schwarze, Jörg; Jung, Britta A; Bourauel, Christoph

2014-06-01

The exact force systems as well as their progressions generated by removable thermoplastic appliances have not been investigated. Thus, the purposes of this experimental study were to quantify the forces and moments delivered by a single aligner and a series of aligners (Invisalign; Align Technology, Santa Clara, Calif) and to investigate the influence of attachments and power ridges on the force transfer. We studied 970 aligners of the Invisalign system (60 series of aligners). The aligners came from 30 consecutive patients, of which 3 tooth movements (incisor torque, premolar derotation, molar distalization) with 20 movements each were analyzed. The 3 movement groups were subdivided so that 10 movements were supported with an attachment and 10 were not. The patients' ClinCheck (Align Technology, Santa Clara, Calif) was planned so that the movements to be investigated were performed in isolation in the respective quadrant. Resin replicas of the patients' intraoral situation before the start of the investigated movement were taken and mounted in a biomechanical measurement system. An aligner was put on the model, the force systems were measured, and the calculated movements were experimentally performed until no further forces or moments were generated. Subsequently, the next aligners were installed, and the measurements were repeated. The initial mean moments were about 7.3 N·mm for maxillary incisor torque and about 1.0 N for distalization. Significant differences in the generated moments were measured in the premolar derotation group, whether they were supported with an attachment (8.8 N·mm) or not (1.2 N·mm). All measurements showed an exponential force change. Apart from a few maximal initial force systems, the forces and moments generated by aligners of the Invisalign system are within the range of orthodontic forces. The force change is exponential while a patient is wearing removable thermoplastic appliances. Copyright © 2014 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

34 CFR 300.160 - Participation in assessments.

Code of Federal Regulations, 2010 CFR

2010-07-01

... assessing the academic progress of students with disabilities under Title I of the ESEA, the alternate...) Are aligned with the State's challenging academic content standards and challenging student academic achievement standards; (ii) If the State has adopted modified academic achievement standards permitted in 34...

34 CFR 300.160 - Participation in assessments.

Code of Federal Regulations, 2011 CFR

2011-07-01

... assessing the academic progress of students with disabilities under Title I of the ESEA, the alternate...) Are aligned with the State's challenging academic content standards and challenging student academic achievement standards; (ii) If the State has adopted modified academic achievement standards permitted in 34...

Exploring the Climate Literacy Development Utilizing a Learning Progressions Approach

NASA Astrophysics Data System (ADS)

Drewes, A.; Breslyn, W.; McGinnis, J. R.; Hestness, E.; Mouza, C.

2017-12-01

Climate change encompasses a broad and complex set of concepts that is often challenging for students and educators. Using a learning progressions framework, in this exploratory study we report our efforts to identify, describe, and organize the development of learners' understanding of climate change in an empirically supported learning progression (LP). The learning progression framework is a well suited analytical tool for investigating how student thinking develops over time (Duschl et al., 2007). Our primary research question is "How do learners progress over time from an initial to a more sophisticated understanding of climate change?"We followed a development process that involved drafting a hypothetical learning progression based on the science education research literature, consensus documents such as the Next Generation Science Standards and the Atlas of Science Literacy. Additionally, we conducted expert reviews with both climate scientists and educational researchers on the content and pedagogical expectations. Data are then collected from learners, which are used to modify the hypothetical learning progression based on how well it describes actual student learning. In this current analysis, we present findings from written assessments (N=294) and in-depth interviews (n=27) with middle school students in which we examine their understanding of the role of human activity, the greenhouse effect as the mechanism of climate change, local and global impacts, and strategies for the adaptation and mitigation of climate change. The culmination of our research is a proposed, empirically supported LP for climate change. Our LP is framed by consideration of four primary constructs: Human Activity, Mechanism, Impacts, and Mitigation and Adaptation. The conditional LP provides a solid foundation for continued research as well as providing urgently needed guidance to the education community on climate change education (for curriculum, instruction, and assessment). Based on consensus documents like NGSS, the research literature, and data collected in our investigation, as well as review by practicing climate scientists and educational researchers, the climate change LP represents a robust and empirically supported description of how climate change understanding develops over time.

Using analogy to learn about phenomena at scales outside human perception.

PubMed

Resnick, Ilyse; Davatzes, Alexandra; Newcombe, Nora S; Shipley, Thomas F

2017-01-01

Understanding and reasoning about phenomena at scales outside human perception (for example, geologic time) is critical across science, technology, engineering, and mathematics. Thus, devising strong methods to support acquisition of reasoning at such scales is an important goal in science, technology, engineering, and mathematics education. In two experiments, we examine the use of analogical principles in learning about geologic time. Across both experiments we find that using a spatial analogy (for example, a time line) to make multiple alignments, and keeping all unrelated components of the analogy held constant (for example, keep the time line the same length), leads to better understanding of the magnitude of geologic time. Effective approaches also include hierarchically and progressively aligning scale information (Experiment 1) and active prediction in making alignments paired with immediate feedback (Experiments 1 and 2).

Comparison of Alignment Correction Angles Between Fixed-Bearing and Mobile-Bearing UKA.

PubMed

Inoue, Atsuo; Arai, Yuji; Nakagawa, Shuji; Inoue, Hiroaki; Yamazoe, Shoichi; Kubo, Toshikazu

2016-01-01

Good outcomes have been reported with both fixed-bearing and mobile-bearing unicompartmental knee arthroplasty (UKA). However, overcorrected alignment could induce the progression of arthritis on the non-arthroplasty side. Changes of limb alignment after UKA with both types of bearings (fixed bearing: 24 knees, mobile bearing: 28 knees) were investigated. The mean difference between the preoperative standing femoral-tibial angle (FTA) and postoperative standing FTA was significantly larger in mobile bearing UKA group. In fixed-bearing UKA, there must be some laxity in MCL tension so that a 2-mm tension gauge can be inserted. In mobile-bearing UKA, appropriate MCL tension is needed to prevent bearing dislocation. This difference in MCL tension may have caused the difference in the correction angle between the groups. Copyright © 2016 Elsevier Inc. All rights reserved.

Ocean Literacy: Tools for Scientists and Educators to use in the Development of Education and Outreach Programs About the Ocean

NASA Astrophysics Data System (ADS)

Strang, C.; Lemus, J.; Schoedinger, S.

2006-12-01

Ocean sciences were idiosyncratically left out of the National Science Education Standards and most state standards, resulting in a decline in the public's attention to ocean issues. Concepts about the ocean are hardly taught in K-12 schools, and hardly appear in K-12 curriculum materials, textbooks, assessments or standards. NGS, COSEE, NMEA, NOAA, the US Commission on Ocean Policy, the Pew Ocean Commission have all urgently called for inclusion of the ocean in science standards as a means to increase ocean literacy nationwide. There has never been consensus, however, about what ocean literacy is or what concepts should be included in future standards. Scientists interested in education and outreach activities have not had a framework to guide them in prioritizing the content they present or in determining how that content fits into the context of what K-12 students and the public need to know about science in general. In 2004, an on-line workshop on Ocean Literacy Through Science Standards began the process of developing consensus about what that framework should include. Approximately 100 ocean scientists and educators participated in the workshop, followed by a series of meetings and extensive review by leading scientists, resulting in a series of draft documents and statements. The importance of community-wide involvement and consensus was reinforced through circulation of the draft documents for public comment April -May, 2005. The community agreed on an Ocean Literacy definition, tagline, seven ocean principles, 44 concepts and a matrix aligning the concepts to the National Science Education Standards (NSES). The elements are described in more detail in the final Ocean Literacy brochure. Broad ownership of the resulting documents is a tribute to the inclusiveness of the process used to develop them. The emerging consensus on Ocean Literacy has become an instrument for change, and has served as an important tool guiding the ocean sciences education efforts of scientists, educators, and most importantly, has provided a common language for scientists and educators working together. In this past year, a similar community-wide effort has been mounted to develop an "Ocean Literacy Scope and Sequence" to serve as a critical companion to "Ocean Literacy: The Essential Principles of Ocean Sciences Grades K-12." The Scope and Sequence shows how the principles and concepts develop and build in logical and developmentally sound learning progressions across grade spans K-12. This document will provide further guidance to teachers, curriculum developers, textbook writers, and ocean scientists, as to what concepts about the ocean are appropriate to introduce at various grade spans. It will show the relationship between the new discoveries of cutting edge science and the basic science concepts on which they are built and which students are accountable to understand. Those concerned about science education and about the future health of the ocean must be poised to influence the development of science standards by local educational agencies, state departments of education and professional societies and associations. In order to be effective, we must have tools, products, documents, web sites that contain agreed upon science content and processes related to the ocean.

WebLogo

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

Crooks, Gavin E.

WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible. Sequesnce logos are a graphical representation of an amino acid or nucleic acid multiple sequence alignment developed by Tom Schneider and Mike Stephens. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. In general, a sequence logo provides a richermore » and more precise description of, for example, a binding site, than would a consensus sequence.« less

Prognostic factors of arthroscopic pull-out repair for a posterior root tear of the medial meniscus.

PubMed

Moon, Hong-Kyo; Koh, Yong-Gon; Kim, Yong-Chan; Park, Young-Sik; Jo, Seung-Bae; Kwon, Sae-Kwang

2012-05-01

Repair of a posterior root tear of the medial meniscus (MRT) decreases peak contact pressure by restoring hoop tension and is expected to prevent progression to osteoarthritis. The purposes of this study were (1) to report the clinical and magnetic resonance imaging (MRI) results of arthroscopic pull-out repair of the MRT and (2) to identify prognostic factors of poor outcome. Case series; Level of evidence, 4. Fifty-one patients (47 women, 4 men) who underwent arthroscopic pull-out repair of the MRT by a single surgeon were enrolled. Mean follow-up after surgery was 33 months (range, 24-44 months). To identify factors affecting final outcome, patient-specific factors, such as gender, age, body mass index, meniscus extrusion, extrusion increase, subchondral edema, degree of varus alignment (<5° or >5°), and cartilage status in the medial compartment (Outerbridge grade 1 or 2 lesion vs grade 3 or 4 lesion), were investigated. Final clinical outcomes were determined using a visual analog scale (VAS) for pain and patient satisfaction scores, American Knee Society (AKS) scores, and Lysholm scores, and MRI outcomes were determined by evaluating meniscus extrusion and articular cartilage status. Multiple regression analysis was performed to identify variables that independently affected clinical and MRI-determined outcomes. All clinical outcome measures significantly improved after surgery. Patients with Outerbridge grade 3 or 4 chondral lesions had poorer results than those with grade 1 or 2 lesions in terms of AKS function and Lysholm scores. Patients with varus alignment of >5° had poorer results than those with varus alignment of <5° in terms of VAS satisfaction, AKS function, and Lysholm scores. Mean meniscus extrusion increased from 3.6 mm preoperatively to 5.0 mm postoperatively. Chondral lesions progressed in 3 (9.7%) of 31 patients. Preoperative meniscus extrusion was found to be positively correlated with final extrusion. At a mean follow-up of 33 months after pull-out repair, extrusion of the meniscus was found to have progressed. Nevertheless, this technique provided patients with a clinical benefit. Outerbridge grade 3 or 4 chondral lesions and varus alignment of >5° were found to independently predict an inferior clinical outcome.

[Delivery management for the prevention of shoulder dystocia in case of identified risk factors].

PubMed

Schmitz, T

2015-12-01

To determine the impact of (i) computed tomographic (CT) pelvimetry for the choice of the mode of delivery, (ii) cesarean, (iii) induction of labor, and of (iv) various delivery managements on the risk of shoulder dystocia in case of fetal macrosomia, with or without maternal diabetes, and in women with previous history of shoulder dystocia. The PubMed database, the Cochrane Library and the recommendations from the French and foreign obstetrical societies or colleges have been consulted. In case of clinically suspected macrosomia, a sonography should be performed to increase diagnostic performances and to assist in decision-making (Professional consensus). Because CT pelvimetry is associated with high false positive rates and increases cesarean deliveries, its use is not recommended to prevent shoulder dystocia in case of fetal macrosomia (Professional consensus). To avoid the neonatal complications of shoulder dystocia, mainly permanent brachial plexus palsy, cesarean delivery is recommended in case of estimated fetal weight (EFW) greater than 4500 g if associated with maternal diabetes (grade C), and greater than 5000 g in the absence of maternal diabetes (grade C). The published data do not provide definitive evidences to recommend systematic labor induction in case of impending fetal macrosomia (Professional consensus). In case of favourable cervix and gestational age greater than 39 weeks of gestation, labor induction should be promoted (Professional consensus). Prophylactic McRoberts maneuver is not recommended to prevent shoulder dystocia in case of fetal macrosomia (grade C). Because data are lacking, no recommendation is possible regarding the use of episiotomy. In case of fetal macrosomia and failure to progress in the second stage of labor, midpelvic and higher instrumental deliveries are not recommended and a cesarean delivery should be preferred (grade C), if the fetal head is at or lower than a +2 station, cesarean delivery is not recommended and an instrumental delivery should be preferred (grade C). Finally, cesarean delivery should be discussed when history of shoulder dystocia has been associated with severe neonatal or maternal complications (Professional consensus). To avoid shoulder dystocia and its complications, only two measures are proposed. Induction of labor is recommended in case of impending macrosomia if the cervix is favourable and gestational age greater than 39 weeks of gestation (Professional consensus). Cesarean delivery is recommended before labor in case of (i) EFW greater than 4500 g if associated with maternal diabetes (grade C), (ii) EFW greater than 5000 g in the absence of maternal diabetes (grade C), and finally (iii) during labor, in case of fetal macrosomia and failure to progress in the second stage, when the fetal head is above a +2 station (grade C). Finally, cesarean delivery should be discussed when history of shoulder dystocia has been associated with severe neonatal or maternal complications (Professional consensus). Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Confronting Dominant Whiteness in the Primary Classroom: Progressive Student Teachers' Dilemmas and Constraints

ERIC Educational Resources Information Center

Pearce, Sarah

2012-01-01

Concerns about new teachers' capacity to address diversity in their classrooms are growing in many parts of the West, and there is some consensus that one aspect of the problem is the narrow range of cultural and social backgrounds from which teacher candidates are drawn. Yet a minority of socially aware teachers, from all backgrounds, continue to…

Modeling visual problem solving as analogical reasoning.

PubMed

Lovett, Andrew; Forbus, Kenneth

2017-01-01

We present a computational model of visual problem solving, designed to solve problems from the Raven's Progressive Matrices intelligence test. The model builds on the claim that analogical reasoning lies at the heart of visual problem solving, and intelligence more broadly. Images are compared via structure mapping, aligning the common relational structure in 2 images to identify commonalities and differences. These commonalities or differences can themselves be reified and used as the input for future comparisons. When images fail to align, the model dynamically rerepresents them to facilitate the comparison. In our analysis, we find that the model matches adult human performance on the Standard Progressive Matrices test, and that problems which are difficult for the model are also difficult for people. Furthermore, we show that model operations involving abstraction and rerepresentation are particularly difficult for people, suggesting that these operations may be critical for performing visual problem solving, and reasoning more generally, at the highest level. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Evolution of Multidisciplinary Translational Teams (MTTs): Insights for Accelerating Translational Innovations

PubMed Central

Calhoun, William J.; Bhavnani, Suresh; Rose, Robert M.; Ameredes, Bill; Brasier, Allan R.

2015-01-01

Abstract There is growing consensus about the factors critical for development and productivity of multidisciplinary teams, but few studies have evaluated their longitudinal changes. We present a longitudinal study of 10 multidisciplinary translational teams (MTTs), based on team process and outcome measures, evaluated before and after 3 years of CTSA collaboration. Using a mixed methods approach, an expert panel of five judges (familiar with the progress of the teams) independently rated team performance based on four process and four outcome measures, and achieved a rating consensus. Although all teams made progress in translational domains, other process and outcome measures were highly variable. The trajectory profiles identified four categories of team performance. Objective bibliometric analysis of CTSA‐supported MTTs with positive growth in process scores showed that these teams tended to have enhanced scientific outcomes and published in new scientific domains, indicating the conduct of innovative science. Case exemplars revealed that MTTs that experienced growth in both process and outcome evaluative criteria also experienced greater innovation, defined as publications in different areas of science. Of the eight evaluative criteria, leadership‐related behaviors were the most resistant to the interventions introduced. Well‐managed MTTs demonstrate objective productivity and facilitate innovation. PMID:25801998

Evolution of Multidisciplinary Translational Teams (MTTs): Insights for Accelerating Translational Innovations.

PubMed

Wooten, Kevin C; Calhoun, William J; Bhavnani, Suresh; Rose, Robert M; Ameredes, Bill; Brasier, Allan R

2015-10-01

There is growing consensus about the factors critical for development and productivity of multidisciplinary teams, but few studies have evaluated their longitudinal changes. We present a longitudinal study of 10 multidisciplinary translational teams (MTTs), based on team process and outcome measures, evaluated before and after 3 years of CTSA collaboration. Using a mixed methods approach, an expert panel of five judges (familiar with the progress of the teams) independently rated team performance based on four process and four outcome measures, and achieved a rating consensus. Although all teams made progress in translational domains, other process and outcome measures were highly variable. The trajectory profiles identified four categories of team performance. Objective bibliometric analysis of CTSA-supported MTTs with positive growth in process scores showed that these teams tended to have enhanced scientific outcomes and published in new scientific domains, indicating the conduct of innovative science. Case exemplars revealed that MTTs that experienced growth in both process and outcome evaluative criteria also experienced greater innovation, defined as publications in different areas of science. Of the eight evaluative criteria, leadership-related behaviors were the most resistant to the interventions introduced. Well-managed MTTs demonstrate objective productivity and facilitate innovation. © 2015 Wiley Periodicals, Inc.

Chinese expert consensus on cytoreductive surgery and hyperthermic intraperitoneal chemotherapy for peritoneal malignancies

PubMed Central

Li, Yan; Zhou, Yun-Feng; Liang, Han; Wang, Hua-Qing; Hao, Ji-Hui; Zhu, Zheng-Gang; Wan, De-Seng; Qin, Lun-Xiu; Cui, Shu-Zhong; Ji, Jia-Fu; Xu, Hui-Mian; Wei, Shao-Zhong; Xu, Hong-Bin; Suo, Tao; Yang, Shu-Jun; Xie, Cong-Hua; Yang, Xiao-Jun; Yang, Guo-Liang

2016-01-01

Locoregional spread of abdominopelvic malignant tumors frequently results in peritoneal carcinomatosis (PC). The prognosis of PC patients treated by conventional systemic chemotherapy is poor, with a median survival of < 6 mo. However, over the past three decades, an integrated treatment strategy of cytoreductive surgery (CRS) + hyperthermic intraperitoneal chemotherapy (HIPEC) has been developed by the pioneering oncologists, with proved efficacy and safety in selected patients. Supported by several lines of clinical evidence from phases I, II and III clinical trials, CRS + HIPEC has been regarded as the standard treatment for selected patients with PC in many established cancer centers worldwide. In China, an expert consensus on CRS + HIPEC has been reached by the leading surgical and medical oncologists, under the framework of the China Anti-Cancer Association. This expert consensus has summarized the progress in PC clinical studies and systematically evaluated the CRS + HIPEC procedures in China as well as across the world, so as to lay the foundation for formulating PC treatment guidelines specific to the national conditions of China. PMID:27570426

A Consensus Action Agenda for Achieving the National Health Information Infrastructure

PubMed Central

Yasnoff, William A.; Humphreys, Betsy L.; Overhage, J. Marc; Detmer, Don E.; Brennan, Patricia Flatley; Morris, Richard W.; Middleton, Blackford; Bates, David W.; Fanning, John P.

2004-01-01

Background: Improving the safety, quality, and efficiency of health care will require immediate and ubiquitous access to complete patient information and decision support provided through a National Health Information Infrastructure (NHII). Methods: To help define the action steps needed to achieve an NHII, the U.S. Department of Health and Human Services sponsored a national consensus conference in July 2003. Results: Attendees favored a public–private coordination group to guide NHII activities, provide education, share resources, and monitor relevant metrics to mark progress. They identified financial incentives, health information standards, and overcoming a few important legal obstacles as key NHII enablers. Community and regional implementation projects, including consumer access to a personal health record, were seen as necessary to demonstrate comprehensive functional systems that can serve as models for the entire nation. Finally, the participants identified the need for increased funding for research on the impact of health information technology on patient safety and quality of care. Individuals, organizations, and federal agencies are using these consensus recommendations to guide NHII efforts. PMID:15187075

Consensus Paper: Roles of the Cerebellum in Motor Control—The Diversity of Ideas on Cerebellar Involvement in Movement

PubMed Central

Bower, James M.; Conforto, Adriana Bastos; Delgado-García, José M.; da Guarda, Suzete Nascimento Farias; Gerwig, Marcus; Habas, Christophe; Hagura, Nobuhiro; Ivry, Richard B.; Mariën, Peter; Molinari, Marco; Naito, Eiichi; Nowak, Dennis A.; Ben Taib, Nordeyn Oulad; Pelisson, Denis; Tesche, Claudia D.; Tilikete, Caroline; Timmann, Dagmar

2015-01-01

Considerable progress has been made in developing models of cerebellar function in sensorimotor control, as well as in identifying key problems that are the focus of current investigation. In this consensus paper, we discuss the literature on the role of the cerebellar circuitry in motor control, bringing together a range of different viewpoints. The following topics are covered: oculomotor control, classical conditioning (evidence in animals and in humans), cerebellar control of motor speech, control of grip forces, control of voluntary limb movements, timing, sensorimotor synchronization, control of corticomotor excitability, control of movement-related sensory data acquisition, cerebro-cerebellar interaction in visuokinesthetic perception of hand movement, functional neuroimaging studies, and magnetoencephalographic mapping of cortico-cerebellar dynamics. While the field has yet to reach a consensus on the precise role played by the cerebellum in movement control, the literature has witnessed the emergence of broad proposals that address cerebellar function at multiple levels of analysis. This paper highlights the diversity of current opinion, providing a framework for debate and discussion on the role of this quintessential vertebrate structure. PMID:22161499

Net2Align: An Algorithm For Pairwise Global Alignment of Biological Networks

PubMed Central

Wadhwab, Gulshan; Upadhyayaa, K. C.

2016-01-01

The amount of data on molecular interactions is growing at an enormous pace, whereas the progress of methods for analysing this data is still lacking behind. Particularly, in the area of comparative analysis of biological networks, where one wishes to explore the similarity between two biological networks, this holds a potential problem. In consideration that the functionality primarily runs at the network level, it advocates the need for robust comparison methods. In this paper, we describe Net2Align, an algorithm for pairwise global alignment that can perform node-to-node correspondences as well as edge-to-edge correspondences into consideration. The uniqueness of our algorithm is in the fact that it is also able to detect the type of interaction, which is essential in case of directed graphs. The existing algorithm is only able to identify the common nodes but not the common edges. Another striking feature of the algorithm is that it is able to remove duplicate entries in case of variable datasets being aligned. This is achieved through creation of a local database which helps exclude duplicate links. In a pervasive computational study on gene regulatory network, we establish that our algorithm surpasses its counterparts in its results. Net2Align has been implemented in Java 7 and the source code is available as supplementary files. PMID:28356678

Efficient and Accurate Algorithm for Cleaved Fragments Prediction (CFPA) in Protein Sequences Dataset Based on Consensus and Its Variants: A Novel Degradomics Prediction Application.

PubMed

El-Assaad, Atlal; Dawy, Zaher; Nemer, Georges; Hajj, Hazem; Kobeissy, Firas H

2017-01-01

Degradomics is a novel discipline that involves determination of the proteases/substrate fragmentation profile, called the substrate degradome, and has been recently applied in different disciplines. A major application of degradomics is its utility in the field of biomarkers where the breakdown products (BDPs) of different protease have been investigated. Among the major proteases assessed, calpain and caspase proteases have been associated with the execution phases of the pro-apoptotic and pro-necrotic cell death, generating caspase/calpain-specific cleaved fragments. The distinction between calpain and caspase protein fragments has been applied to distinguish injury mechanisms. Advanced proteomics technology has been used to identify these BDPs experimentally. However, it has been a challenge to identify these BDPs with high precision and efficiency, especially if we are targeting a number of proteins at one time. In this chapter, we present a novel bioinfromatic detection method that identifies BDPs accurately and efficiently with validation against experimental data. This method aims at predicting the consensus sequence occurrences and their variants in a large set of experimentally detected protein sequences based on state-of-the-art sequence matching and alignment algorithms. After detection, the method generates all the potential cleaved fragments by a specific protease. This space and time-efficient algorithm is flexible to handle the different orientations that the consensus sequence and the protein sequence can take before cleaving. It is O(mn) in space complexity and O(Nmn) in time complexity, with N number of protein sequences, m length of the consensus sequence, and n length of each protein sequence. Ultimately, this knowledge will subsequently feed into the development of a novel tool for researchers to detect diverse types of selected BDPs as putative disease markers, contributing to the diagnosis and treatment of related disorders.

Differential Mechanisms of Activation of the Ang Peptide Receptors AT1, AT2, and MAS: Using In Silico Techniques to Differentiate the Three Receptors

PubMed Central

Prokop, Jeremy W.; Santos, Robson A. S.; Milsted, Amy

2013-01-01

The renin-angiotensin system is involved in multiple conditions ranging from cardiovascular disorders to cancer. Components of the pathway, including ACE, renin and angiotensin receptors are targets for disease treatment. This study addresses three receptors of the pathway: AT1, AT2, and MAS and how the receptors are similar and differ in activation by angiotensin peptides. Combining biochemical and amino acid variation data with multiple species sequence alignments, structural models, and docking site predictions allows for visualization of how angiotensin peptides may bind and activate the receptors; allowing identification of conserved and variant mechanisms in the receptors. MAS differs from AT1 favoring Ang-(1–7) and not Ang II binding, while AT2 recently has been suggested to preferentially bind Ang III. A new model of Ang peptide binding to AT1 and AT2 is proposed that correlates data from site directed mutagenesis and photolabled experiments that were previously considered conflicting. Ang II binds AT1 and AT2 through a conserved initial binding mode involving amino acids 111 (consensus 325) of AT1 (Asn) interacting with Tyr (4) of Ang II and 199 and 256 (consensus 512 and 621, a Lys and His respectively) interacting with Phe (8) of Ang II. In MAS these sites are not conserved, leading to differential binding and activation by Ang-(1–7). In both AT1 and AT2, the Ang II peptide may internalize through Phe (8) of Ang II propagating through the receptors’ conserved aromatic amino acids to the final photolabled positioning relative to either AT1 (amino acid 294, Asn, consensus 725) or AT2 (138, Leu, consensus 336). Understanding receptor activation provides valuable information for drug design and identification of other receptors that can potentially bind Ang peptides. PMID:23755216

Short-chain consensus alpha-neurotoxin: a synthetic 60-mer peptide with generic traits and enhanced immunogenic properties.

PubMed

de la Rosa, Guillermo; Corrales-García, Ligia L; Rodriguez-Ruiz, Ximena; López-Vera, Estuardo; Corzo, Gerardo

2018-07-01

The three-fingered toxin family and more precisely short-chain α-neurotoxins (also known as Type I α-neurotoxins) are crucial in defining the elapid envenomation process, but paradoxically, they are barely neutralized by current elapid snake antivenoms. This work has been focused on the primary structural identity among Type I neurotoxins in order to create a consensus short-chain α-neurotoxin with conserved characteristics. A multiple sequence alignment considering the twelve most toxic short-chain α-neurotoxins reported from the venoms of the elapid genera Acanthophis, Oxyuranus, Walterinnesia, Naja, Dendroaspis and Micrurus led us to propose a short-chain consensus α-neurotoxin, here named ScNtx. The synthetic ScNtx gene was de novo constructed and cloned into the expression vector pQE30 containing a 6His-Tag and an FXa proteolytic cleavage region. Escherichia coli Origami cells transfected with the pQE30/ScNtx vector expressed the recombinant consensus neurotoxin in a soluble form with a yield of 1.5 mg/L of culture medium. The 60-amino acid residue ScNtx contains canonical structural motifs similar to α-neurotoxins from African elapids and its LD 50 of 3.8 µg/mice is similar to the most toxic short-chain α-neurotoxins reported from elapid venoms. Furthermore, ScNtx was also able to antagonize muscular, but not neuronal, nicotinic acetylcholine receptors (nAChR). Rabbits immunized with ScNtx were able to immune-recognize short-chain α-neurotoxins within whole elapid venoms. Type I neurotoxins are difficult to isolate and purify from natural sources; therefore, the heterologous expression of molecules such ScNtx, bearing crucial motifs and key amino acids, is a step forward to create common immunogens for developing cost-effective antivenoms with a wider spectrum of efficacy, quality and strong therapeutic value.

[Consensus conferences in Israel--a collaborative model for national policy making].

PubMed

Tal, Orna; Oberlander, Shira; Siebzehner, Miri I

2014-07-01

The determination of an integrated national policy on controversial issues is a challenge for health systems worldwide. A common method to reach agreements for national policies in different countries throughout the world is group discussion that involves all stakeholders. A structured model of discussion on medical technologies started in the 1970s, mostly in North America, spreading to Europe and in the last decade also crossed borders to India, South America and Israel. Public discussion in the format of a consensus conference is a complex process that includes a thorough literature review for technology assessment, combining academic information using a technique of close consultation with experts, extensive panel discussion and dialogue with representatives of the public. At the end of the process a broad consensus is determined facilitating national-level policy implementation. The multiple factors involved, the issues addressed, the nature of the health system where the intended results will be applied, as well as political and social characteristics, produce variations among different countries. Therefore, this process requires flexibility in adjusting the classic model according to the awakening needs. The advantages of this method include encouraging the appropriate utilization of existing technologies, contemporary assessment by leading experts, aligning between all involved parties, public sharing and more. The initial model of the consensus conference was implemented in an orderly, systematic, structured process which allowed broad discussion, and many factors for thorough preparation. The disadvantages are its complexity, length and cost. In order to cope with the dynamics of the health system in israel, forcing policymakers to make decisions in real time, parts of the model were adjusted to address the issues arising in the system. Hence, a new process was developed--a derivative of the original Israeli model, with an emphasis on professional reviews, group discussion, and involvement of leading factors in the system. The participation of patients and the public in the process requires a thorough examination.

Prevention and management of noncommunicable disease: the IOC Consensus Statement, Lausanne 2013.

PubMed

Matheson, Gordon O; Klügl, Martin; Engebretsen, Lars; Bendiksen, Fredrik; Blair, Steven N; Börjesson, Mats; Budgett, Richard; Derman, Wayne; Erdener, Uğur; Ioannidis, John P A; Khan, Karim M; Martinez, Rodrigo; van Mechelen, Willem; Mountjoy, Margo; Sallis, Robert E; Schwellnus, Martin; Shultz, Rebecca; Soligard, Torbjørn; Steffen, Kathrin; Sundberg, Carl Johan; Weiler, Richard; Ljungqvist, Arne

2013-11-01

Morbidity and mortality from preventable, noncommunicable chronic disease (NCD) threatens the health of our populations and our economies. The accumulation of vast amounts of scientific knowledge has done little to change this. New and innovative thinking is essential to foster new creative approaches that leverage and integrate evidence through the support of big data, technology, and design thinking. The purpose of this paper is to summarize the results of a consensus meeting on NCD prevention sponsored by the International Olympic Committee (IOC) in April 2013. Within the context of advocacy for multifaceted systems change, the IOC's focus is to create solutions that gain traction within health care systems. The group of participants attending the meeting achieved consensus on a strategy for the prevention and management of chronic disease that includes the following: 1. Focus on behavioral change as the core component of all clinical programs for the prevention and management of chronic disease. 2. Establish actual centers to design, implement, study, and improve preventive programs for chronic disease. 3. Use human-centered design (HCD) in the creation of prevention programs with an inclination to action, rapid prototyping and multiple iterations. 4. Extend the knowledge and skills of Sports and Exercise Medicine (SEM) professionals to build new programs for the prevention and treatment of chronic disease focused on physical activity, diet, and lifestyle. 5. Mobilize resources and leverage networks to scale and distribute programs of prevention. True innovation lies in the ability to align thinking around these core strategies to ensure successful implementation of NCD prevention and management programs within health care. The IOC and SEM community are in an ideal position to lead this disruptive change. The outcome of the consensus meeting was the creation of the IOC Non-Communicable Diseases ad hoc Working Group charged with the responsibility of moving this agenda forward.

Prevention and management of non-communicable disease: the IOC consensus statement, Lausanne 2013.

PubMed

Matheson, Gordon O; Klügl, Martin; Engebretsen, Lars; Bendiksen, Fredrik; Blair, Steven N; Börjesson, Mats; Budgett, Richard; Derman, Wayne; Erdener, Uğur; Ioannidis, John P A; Khan, Karim M; Martinez, Rodrigo; van Mechelen, Willem; Mountjoy, Margo; Sallis, Robert E; Schwellnus, Martin; Shultz, Rebecca; Soligard, Torbjørn; Steffen, Kathrin; Sundberg, Carl Johan; Weiler, Richard; Ljungqvist, Arne

2013-11-01

Morbidity and mortality from preventable, non-communicable chronic disease (NCD) threatens the health of our populations and our economies. The accumulation of vast amounts of scientific knowledge has done little to change this. New and innovative thinking is essential to foster new creative approaches that leverage and integrate evidence through the support of big data, technology, and design thinking. The purpose of this paper is to summarize the results of a consensus meeting on NCD prevention sponsored by the International Olympic Committee (IOC) in April, 2013. Within the context of advocacy for multifaceted systems change, the IOC's focus is to create solutions that gain traction within health care systems. The group of participants attending the meeting achieved consensus on a strategy for the prevention and management of chronic disease that includes the following: 1. Focus on behavioural change as the core component of all clinical programs for the prevention and management of chronic disease. 2. Establish actual centres to design, implement, study, and improve preventive programs for chronic disease. 3. Use human-centered design in the creation of prevention programs with an inclination to action, rapid prototyping and multiple iterations. 4. Extend the knowledge and skills of Sports and Exercise Medicine (SEM) professionals to build new programs for the prevention and treatment of chronic disease focused on physical activity, diet and lifestyle. 5. Mobilize resources and leverage networks to scale and distribute programs of prevention. True innovation lies in the ability to align thinking around these core strategies to ensure successful implementation of NCD prevention and management programs within health care. The IOC and SEM community are in an ideal position to lead this disruptive change. The outcome of the consensus meeting was the creation of the IOC Non-Communicable Diseases ad-hoc Working Group charged with the responsibility of moving this agenda forward.

Prevention and management of non-communicable disease: the IOC consensus statement, Lausanne 2013.

PubMed

Matheson, Gordon O; Klügl, Martin; Engebretsen, Lars; Bendiksen, Fredrik; Blair, Steven N; Börjesson, Mats; Budgett, Richard; Derman, Wayne; Erdener, Ugur; Ioannidis, John P A; Khan, Karim M; Martinez, Rodrigo; Van Mechelen, Willem; Mountjoy, Margo; Sallis, Robert E; Schwellnus, Martin; Shultz, Rebecca; Soligard, Torbjørn; Steffen, Kathrin; Sundberg, Carl Johan; Weiler, Richard; Ljungqvist, Arne

2013-11-01

Morbidity and mortality from preventable, non-communicable chronic disease (NCD) threatens the health of our populations and our economies. The accumulation of vast amounts of scientific knowledge has done little to change this. New and innovative thinking is essential to foster new creative approaches that leverage and integrate evidence through the support of big data, technology and design thinking. The purpose of this paper is to summarise the results of a consensus meeting on NCD prevention sponsored by the IOC in April 2013. Within the context of advocacy for multifaceted systems change, the IOC's focus is to create solutions that gain traction within healthcare systems. The group of participants attending the meeting achieved consensus on a strategy for the prevention and management of chronic disease that includes the following: (1) Focus on behavioural change as the core component of all clinical programmes for the prevention and management of chronic disease. (2) Establish actual centres to design, implement, study and improve preventive programmes for chronic disease. (3) Use human-centred design in the creation of prevention programmes with an inclination to action, rapid prototyping and multiple iterations. (4) Extend the knowledge and skills of Sports and Exercise Medicine (SEM) professionals to build new programmes for the prevention and treatment of chronic disease focused on physical activity, diet and lifestyle. (5) Mobilise resources and leverage networks to scale and distribute programmes of prevention. True innovation lies in the ability to align thinking around these core strategies to ensure successful implementation of NCD prevention and management programmes within healthcare. The IOC and SEM community are in an ideal position to lead this disruptive change. The outcome of the consensus meeting was the creation of the IOC Non-Communicable Diseases ad hoc Working Group charged with the responsibility of moving this agenda forward.

Report from a consensus conference on antibody-mediated rejection in heart transplantation

PubMed Central

Kobashigawa, Jon; Crespo-Leiro, Maria G.; Ensminger, Stephan M.; Reichenspurner, Hermann; Angelini, Annalisa; Berry, Gerald; Burke, Margaret; Czer, Lawrence; Hiemann, Nicola; Kfoury, Abdallah G.; Mancini, Donna; Mohacsi, Paul; Patel, Jignesh; Pereira, Naveen; Platt, Jeffrey L.; Reed, Elaine F.; Reinsmoen, Nancy; Rodriguez, E. Rene; Rose, Marlene L.; Russell, Stuart D.; Starling, Randy; Suciu-Foca, Nicole; Tallaj, Jose; Taylor, David O.; Van Bakel, Adrian; West, Lori; Zeevi, Adriana; Zuckermann, Andreas

2012-01-01

BACKGROUND The problem of AMR remains unsolved because standardized schemes for diagnosis and treatment remains contentious. Therefore, a consensus conference was organized to discuss the current status of antibody-mediated rejection (AMR) in heart transplantation. METHODS The conference included 83 participants (transplant cardiologists, surgeons, immunologists and pathologists) representing 67 heart transplant centers from North America, Europe, and Asia who all participated in smaller break-out sessions to discuss the various topics of AMR and attempt to achieve consensus. RESULTS A tentative pathology diagnosis of AMR was established, however, the pathologist felt that further discussion was needed prior to a formal recommendation for AMR diagnosis. One of the most important outcomes of this conference was that a clinical definition for AMR (cardiac dysfunction and/or circulating donor-specific antibody) was no longer believed to be required due to recent publications demonstrating that asymptomatic (no cardiac dysfunction) biopsy-proven AMR is associated with subsequent greater mortality and greater development of cardiac allograft vasculopathy. It was also noted that donor-specific antibody is not always detected during AMR episodes as the antibody may be adhered to the donor heart. Finally, recommendations were made for the timing for specific staining of endomyocardial biopsy specimens and the frequency by which circulating antibodies should be assessed. Recommendations for management and future clinical trials were also provided. CONCLUSIONS The AMR Consensus Conference brought together clinicians, pathologists and immunologists to further the understanding of AMR. Progress was made toward a pathology AMR grading scale and consensus was accomplished regarding several clinical issues. PMID:21300295

Consensus statement for standard of care in spinal muscular atrophy.

PubMed

Wang, Ching H; Finkel, Richard S; Bertini, Enrico S; Schroth, Mary; Simonds, Anita; Wong, Brenda; Aloysius, Annie; Morrison, Leslie; Main, Marion; Crawford, Thomas O; Trela, Anthony

2007-08-01

Spinal muscular atrophy is a neurodegenerative disease that requires multidisciplinary medical care. Recent progress in the understanding of molecular pathogenesis of spinal muscular atrophy and advances in medical technology have not been matched by similar developments in the care for spinal muscular atrophy patients. Variations in medical practice coupled with differences in family resources and values have resulted in variable clinical outcomes that are likely to compromise valid measure of treatment effects during clinical trials. The International Standard of Care Committee for Spinal Muscular Atrophy was formed in 2005, with a goal of establishing practice guidelines for clinical care of these patients. The 12 core committee members worked with more than 60 spinal muscular atrophy experts in the field through conference calls, e-mail communications, a Delphi survey, and 2 in-person meetings to achieve consensus on 5 care areas: diagnostic/new interventions, pulmonary, gastrointestinal/nutrition, orthopedics/rehabilitation, and palliative care. Consensus was achieved on several topics related to common medical problems in spinal muscular atrophy, diagnostic strategies, recommendations for assessment and monitoring, and therapeutic interventions in each care area. A consensus statement was drafted to address the 5 care areas according to 3 functional levels of the patients: nonsitter, sitter, and walker. The committee also identified several medical practices lacking consensus and warranting further investigation. It is the authors' intention that this document be used as a guideline, not as a practice standard for their care. A practice standard for spinal muscular atrophy is urgently needed to help with the multidisciplinary care of these patients.

Consensus on Quality Indicators of Postgraduate Medical E-Learning: Delphi Study

PubMed Central

Walsh, Kieran; Westerman, Michiel; Scheele, Fedde

2018-01-01

Background The progressive use of e-learning in postgraduate medical education calls for useful quality indicators. Many evaluation tools exist. However, these are diversely used and their empirical foundation is often lacking. Objective We aimed to identify an empirically founded set of quality indicators to set the bar for “good enough” e-learning. Methods We performed a Delphi procedure with a group of 13 international education experts and 10 experienced users of e-learning. The questionnaire started with 57 items. These items were the result of a previous literature review and focus group study performed with experts and users. Consensus was met when a rate of agreement of more than two-thirds was achieved. Results In the first round, the participants accepted 37 items of the 57 as important, reached no consensus on 20, and added 15 new items. In the second round, we added the comments from the first round to the items on which there was no consensus and added the 15 new items. After this round, a total of 72 items were addressed and, of these, 37 items were accepted and 34 were rejected due to lack of consensus. Conclusions This study produced a list of 37 items that can form the basis of an evaluation tool to evaluate postgraduate medical e-learning. This is, to our knowledge, the first time that quality indicators for postgraduate medical e-learning have been defined and validated. The next step is to create and validate an e-learning evaluation tool from these items. PMID:29699970

Diagnosis and management of Neuromyelitis Optica Spectrum Disorder (NMOSD) in Iran: A consensus guideline and recommendations.

PubMed

Sahraian, Mohammad Ali; Moghadasi, Abdorreza Naser; Azimi, Amir Reza; Asgari, Nasrin; H Akhoundi, Fahimeh; Abolfazli, Roya; Alaie, Shekoofeh; Ashtari, Fereshteh; Ayromlou, Hormoz; Baghbanian, Seyed Mohammad; Moghadam, Nahid Beladi; Fatehi, Farzad; Foroughipour, Mohsen; Langroodi, Hamidreza Ghalyanchi; Majdinasab, Nastaran; Nickseresht, Alireza; Nourian, Abbas; Shaygannejad, Vahid; Torabi, Hamid Reza

2017-11-01

Neuromyelitis Optica Spectrum Disorder (NMOSD) is a relapsing neuro inflammatory disease of the central nervous system that typically presents with optic neuritis or myelitis and may cause severe disability. The diagnostic criteria have been updated and several immunosuppressive agents have been demonstrated to prevent acute exacerbations. As the disease rarely develops in a progressive course, management of acute attacks and proper prevention of exacerbations may change the long term out-come and prevent future disability. Consensus recommendations and guidelines will help the physicians to improve their practice and unify the treatment approaches in different communities. In order to develop a national consensus and recommendations for the diagnosis and management of NMOSD in Iran, a group of neurologists with long term experience in management of NMOSD were gathered to develop this consensus based on available national and international data. The primary draft was prepared and discussed to suggest the most appropriate treatment for these patients. We propose strategies for early diagnosis and treatment for prevention of relapses and minimizing consequences of attacks as a primary therapeutic goal. Attacks are currently treated with intravenous corticosteroids and, in refractory cases, with plasma exchange. All participants agreed on preventive treatment with currently available immunosuppressive agents such as azothioprin, rituximab and mycofenolate mofetil based on previous positive data in NMOSD in order to reduce attack frequency. The current consensus reviews the previous data and provides the clinicians with practical recommendations and advices for the diagnosis and management of NMOSD based on scientific data and clinical experience. Copyright © 2017 Elsevier B.V. All rights reserved.

French national consensus clinical guidelines for the management of ulcerative colitis.

PubMed

Peyrin-Biroulet, Laurent; Bouhnik, Yoram; Roblin, Xavier; Bonnaud, Guillaume; Hagège, Hervé; Hébuterne, Xavier

2016-07-01

Ulcerative colitis (UC) is a chronic inflammatory bowel disease of multifactorial etiology that primarily affects the colonic mucosa. The disease progresses over time, and clinical management guidelines should reflect its dynamic nature. There is limited evidence supporting UC management in specific clinical situations, thus precluding an evidence-based approach. To use a formal consensus method - the nominal group technique (NGT) - to develop a clinical practice expert opinion to outline simple algorithms and practices, optimize UC management, and assist clinicians in making treatment decisions. The consensus was developed by an expert panel of 37 gastroenterologists from various professional organizations with experience in UC management using the qualitative and iterative NGT, incorporating deliberations based on the European Crohn's and Colitis Organisation recommendations, recent reviews of scientific literature, and pertinent discussion topics developed by a steering committee. Examples of clinical cases for which there are limited evidence-based data from clinical trials were used. Two working groups proposed and voted on treatment algorithms that were then discussed and voted for by the nominal group as a whole, in order to reach a consensus. A clinical practice guideline covering management of the following clinical situations was developed: (i) moderate and severe UC; (ii) acute severe UC; (iii) pouchitis; (iv) refractory proctitis, in the form of treatment algorithms. Given the limited available evidence-based data, a formal consensus methodology was used to develop simple treatment guidelines for UC management in different clinical situations that is now accessible via an online application. Copyright © 2016 Editrice Gastroenterologica Italiana S.r.l. Published by Elsevier Ltd. All rights reserved.

Collagen and collagen-chondroitin sulfate scaffolds with uniaxially aligned pores for the biomimetic, three dimensional culture of trabecular meshwork cells.

PubMed

Osmond, Matthew; Bernier, Sarah M; Pantcheva, Mina B; Krebs, Melissa D

2017-04-01

Glaucoma is a disease in which damage to the optic nerve leads to progressive, irreversible vision loss. The intraocular pressure (IOP) is the only modifiable risk factor for glaucoma and its lowering is considered a useful strategy for preventing or slowing down the progression of glaucomatous neuropathy. Elevated intraocular pressure associated with glaucoma is due to increased aqueous humor outflow resistance, primarily through the trabecular meshwork (TM) of the eye. Current in vitro models of the trabecular meshwork are oversimplified and do not capture the organized and complex three-dimensional nature of this tissue that consists primarily of collagen and glycoasaminoglycans. In this work, collagen and collagen-chondroitin sulfate (CS) scaffolds were fabricated via unidirectional freezing and lyophilization to induce the formation of aligned pores. Scaffolds were characterized by scanning electron microscopy, dynamic mechanical analysis, and a chondroitin sulfate quantification assay. Scaffold characterization confirmed the formation of aligned pores, and also that the CS was leaching out of the scaffolds over time. Primary porcine trabecular meshwork (TM) cells were seeded onto the surface of scaffolds and their gene expression, proliferation, viability, migration into the scaffolds, and morphology were examined. The TM cells were viable and proliferated 2 weeks after seeding. The cells migrated down into the internal scaffold structure and their morphology reflected the topography and alignment of the scaffold structure. This work is a promising step toward the development of a three dimensional in vitro model of the TM that can be used for testing of glaucoma pharmacological agents in future experimentation and to better our understanding of the trabecular meshwork and its complex physiology. Biotechnol. Bioeng. 2017;114: 915-923. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Lessons for major system change: centralization of stroke services in two metropolitan areas of England

PubMed Central

Ramsay, Angus; Perry, Catherine; Boaden, Ruth; McKevitt, Christopher; Morris, Stephen; Pursani, Nanik; Rudd, Anthony; Tyrrell, Pippa; Wolfe, Charles; Fulop, Naomi

2016-01-01

Objectives Our aim was to identify the factors influencing the selection of a model of acute stroke service centralization to create fewer high-volume specialist units in two metropolitan areas of England (London and Greater Manchester). It considers the reasons why services were more fully centralized in London than in Greater Manchester. Methods In both areas, we analysed 316 documents and conducted 45 interviews with people leading transformation, service user organizations, providers and commissioners. Inductive and deductive analyses were used to compare the processes underpinning change in each area, with reference to propositions for achieving major system change taken from a realist review of the existing literature (the Best framework), which we critique and develop further. Results In London, system leadership was used to overcome resistance to centralization and align stakeholders to implement a centralized service model. In Greater Manchester, programme leaders relied on achieving change by consensus and, lacking decision-making authority over providers, accommodated rather than challenged resistance by implementing a less radical transformation of services. Conclusions A combination of system (top-down) and distributed (bottom-up) leadership is important in enabling change. System leadership provides the political authority required to coordinate stakeholders and to capitalize on clinical leadership by aligning it with transformation goals. Policy makers should examine how the structures of system authority, with performance management and financial levers, can be employed to coordinate transformation by aligning the disparate interests of providers and commissioners. PMID:26811375

Lessons for major system change: centralization of stroke services in two metropolitan areas of England.

PubMed

Turner, Simon; Ramsay, Angus; Perry, Catherine; Boaden, Ruth; McKevitt, Christopher; Morris, Stephen; Pursani, Nanik; Rudd, Anthony; Tyrrell, Pippa; Wolfe, Charles; Fulop, Naomi

2016-07-01

Our aim was to identify the factors influencing the selection of a model of acute stroke service centralization to create fewer high-volume specialist units in two metropolitan areas of England (London and Greater Manchester). It considers the reasons why services were more fully centralized in London than in Greater Manchester. In both areas, we analysed 316 documents and conducted 45 interviews with people leading transformation, service user organizations, providers and commissioners. Inductive and deductive analyses were used to compare the processes underpinning change in each area, with reference to propositions for achieving major system change taken from a realist review of the existing literature (the Best framework), which we critique and develop further. In London, system leadership was used to overcome resistance to centralization and align stakeholders to implement a centralized service model. In Greater Manchester, programme leaders relied on achieving change by consensus and, lacking decision-making authority over providers, accommodated rather than challenged resistance by implementing a less radical transformation of services. A combination of system (top-down) and distributed (bottom-up) leadership is important in enabling change. System leadership provides the political authority required to coordinate stakeholders and to capitalize on clinical leadership by aligning it with transformation goals. Policy makers should examine how the structures of system authority, with performance management and financial levers, can be employed to coordinate transformation by aligning the disparate interests of providers and commissioners. © The Author(s) 2016.

MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

PubMed Central

2010-01-01

Background Mass spectrometry (MS) coupled with online separation methods is commonly applied for differential and quantitative profiling of biological samples in metabolomic as well as proteomic research. Such approaches are used for systems biology, functional genomics, and biomarker discovery, among others. An ongoing challenge of these molecular profiling approaches, however, is the development of better data processing methods. Here we introduce a new generation of a popular open-source data processing toolbox, MZmine 2. Results A key concept of the MZmine 2 software design is the strict separation of core functionality and data processing modules, with emphasis on easy usability and support for high-resolution spectra processing. Data processing modules take advantage of embedded visualization tools, allowing for immediate previews of parameter settings. Newly introduced functionality includes the identification of peaks using online databases, MSn data support, improved isotope pattern support, scatter plot visualization, and a new method for peak list alignment based on the random sample consensus (RANSAC) algorithm. The performance of the RANSAC alignment was evaluated using synthetic datasets as well as actual experimental data, and the results were compared to those obtained using other alignment algorithms. Conclusions MZmine 2 is freely available under a GNU GPL license and can be obtained from the project website at: http://mzmine.sourceforge.net/. The current version of MZmine 2 is suitable for processing large batches of data and has been applied to both targeted and non-targeted metabolomic analyses. PMID:20650010

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

Dreimanis, A.

This report considers the problem of multilevel consensus building for siting and construction of shared multinational/regional repositories for radioactive waste (RW) deep disposal. In the siting of a multinational repository there appears an essential innovative component of stakeholder consensus building, namely: to reach consent - political, social, economic, ecological - among international partners, in addition to solving the whole set of intra-national consensus building items. An entire partnering country is considered as a higher-level stakeholder - the national stakeholder, represented by the national government, being faced to simultaneous seeking an upward (international) and a downward (intra-national) consensus in a psychologicallymore » stressed environment, possibly being characterized by diverse political, economic and social interests. The following theses as a possible interdisciplinary approach towards building of shared understanding and stakeholder consensus on the international scale of RW disposal are forwarded and developed: a) building of international stakeholder consensus would be promoted by activating and diversifying on the international scale multilateral interactions between intra- and international stakeholders, including web-based networks of the RW disposal site investigations and decision-making, as well as networks for international cooperation among government authorities in nuclear safety, b) gradual progress in intergovernmental consensus and reaching multilateral agreements on shared deep repositories will be the result of democratic dialogue, via observing the whole set of various interests and common resolving of emerged controversies by using advanced synergetic approaches of conflict resolution, c) cross-cultural thinking and world perception, mental flexibility, creativity and knowledge are considered as basic prerogatives for gaining a higher level of mutual understanding and consensus for seeking further consensus, for advancing the preparedness to act together, and ultimately - for achieving desired shared goals. It is proposed that self-organized social learning will make it possible to promote adequate perception of risk and prevent, by diminishing uncertainties and unknown factors, social amplification of an imagined risk, as well as to increase the trust level and facilitate more adequate equity perception. The proposed approach to the multilevel stakeholder consensus building on international scale is extrapolated to the present-day activities of siting of such near-surface RW disposal facilities which supposedly could have non-negligible trans-boundary impact. A multilevel stakeholder interaction process is considered for the case of resolving of emerged problems in site selection for the planned near-surface RW repository in vicinity of the Lithuanian-Latvian border foreseen for disposal of short lived low- and intermediate level waste arising from the decommissioning of the Ignalina Nuclear Power Plant. (authors)« less

Unsupervised consensus cluster analysis of [18F]-fluoroethyl-L-tyrosine positron emission tomography identified textural features for the diagnosis of pseudoprogression in high-grade glioma

PubMed Central

Kebir, Sied; Khurshid, Zain; Gaertner, Florian C.; Essler, Markus; Hattingen, Elke; Fimmers, Rolf; Scheffler, Björn; Herrlinger, Ulrich; Bundschuh, Ralph A.; Glas, Martin

2017-01-01

Rationale Timely detection of pseudoprogression (PSP) is crucial for the management of patients with high-grade glioma (HGG) but remains difficult. Textural features of O-(2-[18F]fluoroethyl)-L-tyrosine positron emission tomography (FET-PET) mirror tumor uptake heterogeneity; some of them may be associated with tumor progression. Methods Fourteen patients with HGG and suspected of PSP underwent FET-PET imaging. A set of 19 conventional and textural FET-PET features were evaluated and subjected to unsupervised consensus clustering. The final diagnosis of true progression vs. PSP was based on follow-up MRI using RANO criteria. Results Three robust clusters have been identified based on 10 predominantly textural FET-PET features. None of the patients with PSP fell into cluster 2, which was associated with high values for textural FET-PET markers of uptake heterogeneity. Three out of 4 patients with PSP were assigned to cluster 3 that was largely associated with low values of textural FET-PET features. By comparison, tumor-to-normal brain ratio (TNRmax) at the optimal cutoff 2.1 was less predictive of PSP (negative predictive value 57% for detecting true progression, p=0.07 vs. 75% with cluster 3, p=0.04). Principal Conclusions Clustering based on textural O-(2-[18F]fluoroethyl)-L-tyrosine PET features may provide valuable information in assessing the elusive phenomenon of pseudoprogression. PMID:28030820

Dynamic simulation modelling of policy responses to reduce alcohol-related harms: rationale and procedure for a participatory approach.

PubMed

Atkinson, Jo-An; O'Donnell, Eloise; Wiggers, John; McDonnell, Geoff; Mitchell, Jo; Freebairn, Louise; Indig, Devon; Rychetnik, Lucie

2017-02-15

Development of effective policy responses to address complex public health problems can be challenged by a lack of clarity about the interaction of risk factors driving the problem, differing views of stakeholders on the most appropriate and effective intervention approaches, a lack of evidence to support commonly implemented and acceptable intervention approaches, and a lack of acceptance of effective interventions. Consequently, political considerations, community advocacy and industry lobbying can contribute to a hotly contested debate about the most appropriate course of action; this can hinder consensus and give rise to policy resistance. The problem of alcohol misuse and its associated harms in New South Wales (NSW), Australia, provides a relevant example of such challenges. Dynamic simulation modelling is increasingly being valued by the health sector as a robust tool to support decision making to address complex problems. It allows policy makers to ask 'what-if' questions and test the potential impacts of different policy scenarios over time, before solutions are implemented in the real world. Participatory approaches to modelling enable researchers, policy makers, program planners, practitioners and consumer representatives to collaborate with expert modellers to ensure that models are transparent, incorporate diverse evidence and perspectives, are better aligned to the decision-support needs of policy makers, and can facilitate consensus building for action. This paper outlines a procedure for embedding stakeholder engagement and consensus building in the development of dynamic simulation models that can guide the development of effective, coordinated and acceptable policy responses to complex public health problems, such as alcohol-related harms in NSW.

Structural basis for lack of ADP-ribosyltransferase activity in poly(ADP-ribose) polymerase-13/zinc finger antiviral protein.

PubMed

Karlberg, Tobias; Klepsch, Mirjam; Thorsell, Ann-Gerd; Andersson, C David; Linusson, Anna; Schüler, Herwig

2015-03-20

The mammalian poly(ADP-ribose) polymerase (PARP) family includes ADP-ribosyltransferases with diphtheria toxin homology (ARTD). Most members have mono-ADP-ribosyltransferase activity. PARP13/ARTD13, also called zinc finger antiviral protein, has roles in viral immunity and microRNA-mediated stress responses. PARP13 features a divergent PARP homology domain missing a PARP consensus sequence motif; the domain has enigmatic functions and apparently lacks catalytic activity. We used x-ray crystallography, molecular dynamics simulations, and biochemical analyses to investigate the structural requirements for ADP-ribosyltransferase activity in human PARP13 and two of its functional partners in stress granules: PARP12/ARTD12, and PARP15/BAL3/ARTD7. The crystal structure of the PARP homology domain of PARP13 shows obstruction of the canonical active site, precluding NAD(+) binding. Molecular dynamics simulations indicate that this closed cleft conformation is maintained in solution. Introducing consensus side chains in PARP13 did not result in 3-aminobenzamide binding, but in further closure of the site. Three-dimensional alignment of the PARP homology domains of PARP13, PARP12, and PARP15 illustrates placement of PARP13 residues that deviate from the PARP family consensus. Introducing either one of two of these side chains into the corresponding positions in PARP15 abolished PARP15 ADP-ribosyltransferase activity. Taken together, our results show that PARP13 lacks the structural requirements for ADP-ribosyltransferase activity. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Nanoplatforms for highly sensitive fluorescence detection of cancer-related proteases.

PubMed

Wang, Hongwang; Udukala, Dinusha N; Samarakoon, Thilani N; Basel, Matthew T; Kalita, Mausam; Abayaweera, Gayani; Manawadu, Harshi; Malalasekera, Aruni; Robinson, Colette; Villanueva, David; Maynez, Pamela; Bossmann, Leonie; Riedy, Elizabeth; Barriga, Jenny; Wang, Ni; Li, Ping; Higgins, Daniel A; Zhu, Gaohong; Troyer, Deryl L; Bossmann, Stefan H

2014-02-01

Numerous proteases are known to be necessary for cancer development and progression including matrix metalloproteinases (MMPs), tissue serine proteases, and cathepsins. The goal of this research is to develop an Fe/Fe3O4 nanoparticle-based system for clinical diagnostics, which has the potential to measure the activity of cancer-associated proteases in biospecimens. Nanoparticle-based "light switches" for measuring protease activity consist of fluorescent cyanine dyes and porphyrins that are attached to Fe/Fe3O4 nanoparticles via consensus sequences. These consensus sequences can be cleaved in the presence of the correct protease, thus releasing a fluorescent dye from the Fe/Fe3O4 nanoparticle, resulting in highly sensitive (down to 1 × 10(-16) mol l(-1) for 12 proteases), selective, and fast nanoplatforms (required time: 60 min).

Accelerated Math[TM]. What Works Clearinghouse Intervention Report

ERIC Educational Resources Information Center

What Works Clearinghouse, 2011

2011-01-01

"Accelerated Math"[TM], published by Renaissance Learning, is a software tool used to customize assignments and monitor progress in math for students in grades 1-12. The "Accelerated Math"[TM] software creates individualized assignments aligned with state standards and national guidelines, scores student work, and generates…

Authentic leadership: becoming and remaining an authentic nurse leader.

PubMed

Murphy, Lin G

2012-11-01

This article explores how chief nurse executives became and remained authentic leaders. Using narrative inquiry, this qualitative study focused on the life stories of participants. Results demonstrate the importance of reframing, reflection in alignment with values, and the courage needed as nurse leaders progress to authenticity.

Perspective, March 2010

ERIC Educational Resources Information Center

Achieve, Inc., 2010

2010-01-01

"Perspective" is a monthly e-newsletter presenting news and views from Achieve. This month's issue commences with a report stating how over the past five years, since the National Governors Association (NGA) and Achieve co-sponsored the National Education Summit on High Schools, states have made impressive progress in aligning their high…

Mediolateral force distribution at the knee joint shifts across activities and is driven by tibiofemoral alignment.

PubMed

Kutzner, I; Bender, A; Dymke, J; Duda, G; von Roth, P; Bergmann, G

2017-06-01

Tibiofemoral alignment is important to determine the rate of progression of osteoarthritis and implant survival after total knee arthroplasty (TKA). Normally, surgeons aim for neutral tibiofemoral alignment following TKA, but this has been questioned in recent years. The aim of this study was to evaluate whether varus or valgus alignment indeed leads to increased medial or lateral tibiofemoral forces during static and dynamic weight-bearing activities. Tibiofemoral contact forces and moments were measured in nine patients with instrumented knee implants. Medial force ratios were analysed during nine daily activities, including activities with single-limb support (e.g. walking) and double-limb support (e.g. knee bend). Hip-knee-ankle angles in the frontal plane were analysed using full-leg coronal radiographs. The medial force ratio strongly correlated with the tibiofemoral alignment in the static condition of one-legged stance (R² = 0.88) and dynamic single-limb loading (R² = 0.59) with varus malalignment leading to increased medial force ratios of up to 88%. In contrast, the correlation between leg alignment and magnitude of medial compartment force was much less pronounced. A lateral shift of force occurred during activities with double-limb support and higher knee flexion angles. The medial force ratio depends on both the tibiofemoral alignment and the nature of the activity involved. It cannot be generalised to a single value. Higher medial ratios during single-limb loading are associated with varus malalignment in TKA. The current trend towards a 'constitutional varus' after joint replacement, in terms of overall tibiofemoral alignment, should be considered carefully with respect to the increased medial force ratio. Cite this article: Bone Joint J 2017;99-B:779-87. ©2017 The British Editorial Society of Bone & Joint Surgery.

Media Coverage of Alcohol Issues: A Critical Political Economy Framework—A Case Study from Ireland

PubMed Central

Mercille, Julien

2017-01-01

There is a growing literature on news media representations of alcohol-related issues. However, current scholarship has neglected critical political economic frameworks to interpret media coverage of alcohol. This paper presents such a framework that conceives of news organisations as corporations that share the values and interests of political and economic elites. The media are thus expected to present viewpoints that are more aligned with the alcohol industry than the scientific consensus on public health policy would warrant. The media are also expected, but to a lesser extent, to present a certain amount of support for public health perspectives because these are supported by a few socioeconomic elite groups (the medical professions, progressive politicians). The case of Ireland from 2012 to 2017 illustrates the framework empirically. Four main newspapers’ coverage of the Public Health (Alcohol) Bill and related policies is examined. Results show that, overall, 44.0% of articles support public health measures and 56.0% are opposed or remain neutral. It is argued that the media are not strong proponents of public health for multiple reasons: there are more articles opposed to or neutral toward public health measures than supporting them; the number of supportive articles remains relatively small and there are still many pieces presenting drinks industry views; there are virtually no calls in the media for stronger measures; supportive coverage is partially explained by the pub owners lobby’s support for minimum unit pricing; the media often downplay or ignore the negative consequences of alcohol, such as its role in accidents; many news articles normalise drinking and promote events sponsored by the industry; there is not a single Irish journalist covering alcohol issues systematically; and other policy issues that are prioritised by elites receive multiple times more media coverage than public health measures. In short, the media reflect the views of the political and economic establishment on public health measures: there is some support from the medical professions and progressive politicians, but overall, there is a clear reluctance to support strong public health strategies. One main recommendation for public health advocates to promote their perspectives is to diversify the mass media and make them less commercial in nature, as well as to engage with non-corporate, so-called progressive “alternative media” outlets. PMID:28621753

Media Coverage of Alcohol Issues: A Critical Political Economy Framework-A Case Study from Ireland.

PubMed

Mercille, Julien

2017-06-16

There is a growing literature on news media representations of alcohol-related issues. However, current scholarship has neglected critical political economic frameworks to interpret media coverage of alcohol. This paper presents such a framework that conceives of news organisations as corporations that share the values and interests of political and economic elites. The media are thus expected to present viewpoints that are more aligned with the alcohol industry than the scientific consensus on public health policy would warrant. The media are also expected, but to a lesser extent, to present a certain amount of support for public health perspectives because these are supported by a few socioeconomic elite groups (the medical professions, progressive politicians). The case of Ireland from 2012 to 2017 illustrates the framework empirically. Four main newspapers' coverage of the Public Health (Alcohol) Bill and related policies is examined. Results show that, overall, 44.0% of articles support public health measures and 56.0% are opposed or remain neutral. It is argued that the media are not strong proponents of public health for multiple reasons: there are more articles opposed to or neutral toward public health measures than supporting them; the number of supportive articles remains relatively small and there are still many pieces presenting drinks industry views; there are virtually no calls in the media for stronger measures; supportive coverage is partially explained by the pub owners lobby's support for minimum unit pricing; the media often downplay or ignore the negative consequences of alcohol, such as its role in accidents; many news articles normalise drinking and promote events sponsored by the industry; there is not a single Irish journalist covering alcohol issues systematically; and other policy issues that are prioritised by elites receive multiple times more media coverage than public health measures. In short, the media reflect the views of the political and economic establishment on public health measures: there is some support from the medical professions and progressive politicians, but overall, there is a clear reluctance to support strong public health strategies. One main recommendation for public health advocates to promote their perspectives is to diversify the mass media and make them less commercial in nature, as well as to engage with non-corporate, so-called progressive "alternative media" outlets.

RNA-Seq analysis and transcriptome assembly for blackberry (Rubus sp. Var. Lochness) fruit.

PubMed

Garcia-Seco, Daniel; Zhang, Yang; Gutierrez-Mañero, Francisco J; Martin, Cathie; Ramos-Solano, Beatriz

2015-01-22

There is an increasing interest in berries, especially blackberries in the diet, because of recent reports of their health benefits due to their high content of flavonoids. A broad range of genomic tools are available for other Rosaceae species but these tools are still lacking in the Rubus genus, thus limiting gene discovery and the breeding of improved varieties. De novo RNA-seq of ripe blackberries grown under field conditions was performed using Illumina Hiseq 2000. Almost 9 billion nucleotide bases were sequenced in total. Following assembly, 42,062 consensus sequences were detected. For functional annotation, 33,040 (NR), 32,762 (NT), 21,932 (Swiss-Prot), 20,134 (KEGG), 13,676 (COG), 24,168 (GO) consensus sequences were annotated using different databases; in total 34,552 annotated sequences were identified. For protein prediction analysis, the number of coding DNA sequences (CDS) that mapped to the protein database was 32,540. Non redundant (NR), annotation showed that 25,418 genes (73.5%) has the highest similarity with Fragaria vesca subspecies vesca. Reanalysis was undertaken by aligning the reads with this reference genome for a deeper analysis of the transcriptome. We demonstrated that de novo assembly, using Trinity and later annotation with Blast using different databases, were complementary to alignment to the reference sequence using SOAPaligner/SOAP2. The Fragaria reference genome belongs to a species in the same family as blackberry (Rosaceae) but to a different genus. Since blackberries are tetraploids, the possibility of artefactual gene chimeras resulting from mis-assembly was tested with one of the genes sequenced by RNAseq, Chalcone Synthase (CHS). cDNAs encoding this protein were cloned and sequenced. Primers designed to the assembled sequences accurately distinguished different contigs, at least for chalcone synthase genes. We prepared and analysed transcriptome data from ripe blackberries, for which prior genomic information was limited. This new sequence information will improve the knowledge of this important and healthy fruit, providing an invaluable new tool for biological research.

Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.

PubMed

Wymant, Chris; Blanquart, François; Golubchik, Tanya; Gall, Astrid; Bakker, Margreet; Bezemer, Daniela; Croucher, Nicholas J; Hall, Matthew; Hillebregt, Mariska; Ong, Swee Hoe; Ratmann, Oliver; Albert, Jan; Bannert, Norbert; Fellay, Jacques; Fransen, Katrien; Gourlay, Annabelle; Grabowski, M Kate; Gunsenheimer-Bartmeyer, Barbara; Günthard, Huldrych F; Kivelä, Pia; Kouyos, Roger; Laeyendecker, Oliver; Liitsola, Kirsi; Meyer, Laurence; Porter, Kholoud; Ristola, Matti; van Sighem, Ard; Berkhout, Ben; Cornelissen, Marion; Kellam, Paul; Reiss, Peter; Fraser, Christophe

2018-01-01

Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between- and within-host diversity, including frequent indels, may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions. De novo assembly avoids this bias by aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the tool shiver to pre-process reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with the user's choice of existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We used shiver to reconstruct the consensus sequence and minority variant information from paired-end short-read whole-genome data produced with the Illumina platform, for sixty-five existing publicly available samples and fifty new samples. We show the systematic superiority of mapping to shiver's constructed reference compared with mapping the same reads to the closest of 3,249 real references: median values of 13 bases called differently and more accurately, 0 bases called differently and less accurately, and 205 bases of missing sequence recovered. We also successfully applied shiver to whole-genome samples of Hepatitis C Virus and Respiratory Syncytial Virus. shiver is publicly available from https://github.com/ChrisHIV/shiver.

The functional neuroanatomy of bipolar disorder: a consensus model

PubMed Central

Strakowski, Stephen M; Adler, Caleb M; Almeida, Jorge; Altshuler, Lori L; Blumberg, Hilary P; Chang, Kiki D; DelBello, Melissa P; Frangou, Sophia; McIntosh, Andrew; Phillips, Mary L; Sussman, Jessika E; Townsend, Jennifer D

2013-01-01

Objectives Functional neuroimaging methods have proliferated in recent years, such that functional magnetic resonance imaging, in particular, is now widely used to study bipolar disorder. However, discrepant findings are common. A workgroup was organized by the Department of Psychiatry, University of Cincinnati (Cincinnati, OH, USA) to develop a consensus functional neuroanatomic model of bipolar I disorder based upon the participants’ work as well as that of others. Methods Representatives from several leading bipolar disorder neuroimaging groups were organized to present an overview of their areas of expertise as well as focused reviews of existing data. The workgroup then developed a consensus model of the functional neuroanatomy of bipolar disorder based upon these data. Results Among the participants, a general consensus emerged that bipolar I disorder arises from abnormalities in the structure and function of key emotional control networks in the human brain. Namely, disruption in early development (e.g., white matter connectivity, prefrontal pruning) within brain networks that modulate emotional behavior leads to decreased connectivity among ventral prefrontal networks and limbic brain regions, especially amygdala. This developmental failure to establish healthy ventral prefrontal–limbic modulation underlies the onset of mania and ultimately, with progressive changes throughout these networks over time and with affective episodes, a bipolar course of illness. Conclusions This model provides a potential substrate to guide future investigations and areas needing additional focus are identified. PMID:22631617

Ion Conduction in Microphase-Separated Block Copolymer Electrolytes

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

Kambe, Yu; Arges, Christopher G.; Patel, Shrayesh

2017-01-01

Microphase separation of block copolymers provides a promising route towards engineering a mechanically robust ion conducting film for electrochemical devices. The separation into two different nano-domains enables the film to simultaneously exhibit both high ion conductivity and mechanical robustness, material properties inversely related in most homopolymer and random copolymer electrolytes. To exhibit the maximum conductivity and mechanical robustness, both domains would span across macroscopic length scales enabling uninterrupted ion conduction. One way to achieve this architecture is through external alignment fields that are applied during the microphase separation process. In this review, we present the progress and challenges for aligningmore » the ionic domains in block copolymer electrolytes. A survey of alignment and characterization is followed by a discussion of how the nanoscale architecture affects the bulk conductivity and how alignment may be improved to maximize the number of participating conduction domains.« less

Shared Curriculum Model: A Promising Practice for Education Transformation.

PubMed

Close, Liz; Gorski, Mary Sue; Sroczynski, Maureen; Farmer, Pat; Wortock, Jean

2015-12-01

The shared curriculum model is one of four successful models of academic progression identified through a consensus-building process facilitated by The Future of Nursing: Campaign for Action, with support from the Robert Wood Johnson Foundation, AARP, and the AARP Foundation. Seamless academic progression from the associate degree in nursing (ADN) to the baccalaureate degree in nursing (BSN) is achieved either by simultaneously revising both ADN and BSN curricula or by making targeted adjustments in ADN or BSN curricula to create a unified academic progression. Systematic vetting and definitive agreement on nursing prerequisites and corequisites, general education courses, nursing major content, and general degree requirements are necessary to ensure coordinated degree progression. A standardized set of expectations for beginning professional practice and for unique baccalaureate nursing knowledge ensures vital nursing content across the ADN-to-BSN continuum. Examples of state and regional ADN-to-BSN progression programs using the shared curriculum model are highlighted. The shared curriculum model is a promising practical and sustainable approach to seamless ADN-to-BSN academic progression. Copyright 2015, SLACK Incorporated.

A model to begin to use clinical outcomes in medical education.

PubMed

Haan, Constance K; Edwards, Fred H; Poole, Betty; Godley, Melissa; Genuardi, Frank J; Zenni, Elisa A

2008-06-01

The latest phase of the Accreditation Council for Graduate Medical Education (ACGME) Outcome Project challenges graduate medical education (GME) programs to select meaningful clinical quality indicators by which to measure trainee performance and progress, as well as to assess and improve educational effectiveness of programs. The authors describe efforts to measure educational quality, incorporating measurable patient-care outcomes to guide improvement. University of Florida College of Medicine-Jacksonville education leaders developed a tiered framework for selecting clinical indicators whose outcomes would illustrate integration of the ACGME competencies and their assessment with learning and clinical care. In order of preference, indicators selected should align with a specialty's (1) national benchmarked consensus standards, (2) national specialty society standards, (3) standards of local, institutional, or regional quality initiatives, or (4) top-priority diagnostic and/or therapeutic categories for the specialty, based on areas of high frequency, impact, or cost. All programs successfully applied the tiered process to clinical indicator selection and then identified data sources to track clinical outcomes. Using clinical outcomes in resident evaluation assesses the resident's performance as reflective of his or her participation in the health care delivery team. Programmatic improvements are driven by clinical outcomes that are shown to be below benchmark across the residents. Selecting appropriate clinical indicators-representative of quality of care and of graduate medical education-is the first step toward tracking educational outcomes using clinical data as the basis for evaluation and improvement. This effort is an important aspect of orienting trainees to using data for monitoring and improving care processes and outcomes throughout their careers.

Implementation of Duchenne Muscular Dystrophy Care Considerations.

PubMed

Andrews, Jennifer G; Conway, Kristin; Westfield, Christina; Trout, Christina; Meaney, F John; Mathews, Katherine; Ciafaloni, Emma; Cunniff, Christopher; Fox, Deborah J; Matthews, Dennis; Pandya, Shree

2018-06-20

Duchenne muscular dystrophy (DMD) is an X-linked disorder characterized by progressive muscle weakness and multisystem involvement. Recent advances in management of individuals with DMD have prolonged survival. Lack of standardized care spurred an international collaboration to develop consensus-based care considerations for diagnosis and management. In this study, we evaluate adherence to considerations at selected sites. We collaborated with the Muscular Dystrophy Surveillance, Tracking, and Research Network. Our sample included males with DMD and Becker muscular dystrophy <21 years as of December 31, 2010, with 1 health care encounter on or after January 1, 2012. We collected data from medical records on encounters occurring January 1, 2012, through December 31, 2014. Adherence was determined when frequency of visits or assessments were at or above recommendations for selected care considerations. Our analytic sample included 299 individuals, 7% of whom (20/299) were classified as childhood-onset Becker muscular dystrophy. Adherence for neuromuscular and respiratory clinician visits was 65% for the cohort; neuromuscular assessments and corticosteroid side effect monitoring measures ranged from 16% to 68%. Adherence was 83% for forced vital capacity and ≤58% for other respiratory diagnostics. Cardiologist assessments and echocardiograms were found for at least 84%. Transition planning for education or health care was documented for 31% of eligible males. Medical records data were used to identify areas in which practice aligns with the care considerations. However, there remains inconsistency across domains and insufficiency in critical areas. More research is needed to explain this variability and identify reliable methods to measure outcomes. Copyright © 2018 by the American Academy of Pediatrics.

Recent Observational Progress on Accretion Disks Around Compact Objects

NASA Astrophysics Data System (ADS)

Miller, Jon M.

2016-04-01

Studies of accretion disks around black holes and neutron stars over the last ten years have made remarkable progress. Our understanding of disk evolution as a function of mass accretion rate is pushing toward a consensus on thin/thick disk transitions; an apparent switching between disk-driven outflow modes has emerged; and monitoring observations have revealed complex spectral energy distributions wherein disk reprocessing must be important. Detailed studies of disk winds, in particular, have the potential to reveal the basic physical processes that mediate disk accretion, and to connect with numerical simulations. This talk will review these developments and look ahead to the potential of Astro-H.

Development of a reinforced electrochemically aligned collagen bioscaffold for tendon tissue engineering applications

NASA Astrophysics Data System (ADS)

Uquillas Paredes, Jorge Alfredo

Type-I collagen is a promising biomaterial that can be used to synthesize bioscaffolds as a strategy to regenerate and repair damaged tendons. The existing in vitro prepared collagen bioscaffolds are in the form of gels, foams, or extruded fibers. These bioscaffolds readily present sites for attachment of biological factors and cells; however, they have extremely poor biomechanical properties in comparison to the properties of native tendons. The biomechanical function of type-I collagen bioscaffolds needs to be elevated to the level of natural tissues for this biomaterial to replace mechanically challenged tendons in a functionally meaningful way. The overall goal of this dissertation is to develop a reinforced electrochemically aligned collagenous bioscaffold for applications in tendon tissue engineering. The bioscaffold is synthesized by a unique electrochemical process via isoelectric focusing (IEF) to attain a very high degree of molecular alignment and packing density. This dissertation presents progress made on four aims: A) development of simple and descriptive electrochemical theory via the mathematical model of IEF and the forces acting on collagen alignment under an electric field; B) optimization of the post-alignment PBS treatment step to achieve d- banding pattern in uncrosslinked electrochemically aligned collagen (ELAC) bioscaffolds; C) optimization of the best crosslinking protocol to produce the strongest possible ELAC biomaterial with excellent cellular compatibility; and D) in vivo evaluation of the biocompatibility and biodegradability properties of electronically aligned collagen bioscaffolds. The results of this dissertation provide strong evidence showing that reinforced ELAC bioscaffolds could be used clinically in the future to repair damaged tendons.

Scanning laser reflection tool for alignment and period measurement of critical-angle transmission gratings

NASA Astrophysics Data System (ADS)

Song, Jungki; Heilmann, Ralf K.; Bruccoleri, Alexander R.; Hertz, Edward; Schatternburg, Mark L.

2017-08-01

We report progress toward developing a scanning laser reflection (LR) tool for alignment and period measurement of critical-angle transmission (CAT) gratings. It operates on a similar measurement principle as a tool built in 1994 which characterized period variations of grating facets for the Chandra X-ray Observatory. A specularly reflected beam and a first-order diffracted beam were used to record local period variations, surface slope variations, and grating line orientation. In this work, a normal-incidence beam was added to measure slope variations (instead of the angled-incidence beam). Since normal incidence reflection is not coupled with surface height change, it enables measurement of slope variations more accurately and, along with the angled-incidence beam, helps to reconstruct the surface figure (or tilt) map. The measurement capability of in-grating period variations was demonstrated by measuring test reflection grating (RG) samples that show only intrinsic period variations of the interference lithography process. Experimental demonstration for angular alignment of CAT gratings is also presented along with a custom-designed grating alignment assembly (GAA) testbed. All three angles were aligned to satisfy requirements for the proposed Arcus mission. The final measurement of roll misalignment agrees with the roll measurements performed at the PANTER x-ray test facility.

A regional consensus recommendation on brain atrophy as an outcome measure in multiple sclerosis.

PubMed

Alroughani, Raed; Deleu, Dirk; El Salem, Khalid; Al-Hashel, Jasem; Alexander, K John; Abdelrazek, Mohamed Assem; Aljishi, Adel; Alkhaboori, Jaber; Al Azri, Faisal; Al Zadjali, Nahida; Hbahbih, Majed; Sokrab, Tag Eldin; Said, Mohamed; Rovira, Àlex

2016-11-24

Multiple sclerosis (MS) is a chronic autoimmune disease characterized by inflammatory and neurodegenerative processes leading to irreversible neurological impairment. Brain atrophy occurs early in the course of the disease at a rate greater than the general population. Brain volume loss (BVL) is associated with disability progression and cognitive impairment in patients with MS; hence its value as a potential target in monitoring and treating MS is discussed. A group of MS neurologists and neuro-radiologists reviewed the current literature on brain atrophy and discussed the challenges in assessing and implementing brain atrophy measurements in clinical practice. The panel used a voting system to reach a consensus and the votes were counted for the proposed set of questions for cognitive and brain atrophy assessments. The panel of experts was able to identify recent studies, which demonstrated the correlation between BVL and future worsening of disability and cognition. The current evidence revealed that reduction of BVL could be achieved with different disease-modifying therapies (DMTs). BVL provided a better treatment and monitoring strategy when it is combined to the composite measures of "no evidence of disease activity" (NEDA). The panel recommended a set of cognitive assessment tools and MRI methods and software applications that may help in capturing and measuring the underlying MS pathology with high degree of specificity. BVL was considered to be a useful measurement to longitudinally assess disease progression and cognitive function in patients with MS. Brain atrophy measurement was recommended to be incorporated into the concept of NEDA. Consequently, a consensus recommendation was reached in anticipation for implementation of the use of cognitive assessment and brain atrophy measurements on a regional level.

Primate amygdala neurons evaluate the progress of self-defined economic choice sequences

PubMed Central

Grabenhorst, Fabian; Hernadi, Istvan; Schultz, Wolfram

2016-01-01

The amygdala is a prime valuation structure yet its functions in advanced behaviors are poorly understood. We tested whether individual amygdala neurons encode a critical requirement for goal-directed behavior: the evaluation of progress during sequential choices. As monkeys progressed through choice sequences toward rewards, amygdala neurons showed phasic, gradually increasing responses over successive choice steps. These responses occurred in the absence of external progress cues or motor preplanning. They were often specific to self-defined sequences, typically disappearing during instructed control sequences with similar reward expectation. Their build-up rate reflected prospectively the forthcoming choice sequence, suggesting adaptation to an internal plan. Population decoding demonstrated a high-accuracy progress code. These findings indicate that amygdala neurons evaluate the progress of planned, self-defined behavioral sequences. Such progress signals seem essential for aligning stepwise choices with internal plans. Their presence in amygdala neurons may inform understanding of human conditions with amygdala dysfunction and deregulated reward pursuit. DOI: http://dx.doi.org/10.7554/eLife.18731.001 PMID:27731795

Primate amygdala neurons evaluate the progress of self-defined economic choice sequences.

PubMed

Grabenhorst, Fabian; Hernadi, Istvan; Schultz, Wolfram

2016-10-12

The amygdala is a prime valuation structure yet its functions in advanced behaviors are poorly understood. We tested whether individual amygdala neurons encode a critical requirement for goal-directed behavior: the evaluation of progress during sequential choices. As monkeys progressed through choice sequences toward rewards, amygdala neurons showed phasic, gradually increasing responses over successive choice steps. These responses occurred in the absence of external progress cues or motor preplanning. They were often specific to self-defined sequences, typically disappearing during instructed control sequences with similar reward expectation. Their build-up rate reflected prospectively the forthcoming choice sequence, suggesting adaptation to an internal plan. Population decoding demonstrated a high-accuracy progress code. These findings indicate that amygdala neurons evaluate the progress of planned, self-defined behavioral sequences. Such progress signals seem essential for aligning stepwise choices with internal plans. Their presence in amygdala neurons may inform understanding of human conditions with amygdala dysfunction and deregulated reward pursuit.

Tweaked residual convolutional network for face alignment

NASA Astrophysics Data System (ADS)

Du, Wenchao; Li, Ke; Zhao, Qijun; Zhang, Yi; Chen, Hu

2017-08-01

We propose a novel Tweaked Residual Convolutional Network approach for face alignment with two-level convolutional networks architecture. Specifically, the first-level Tweaked Convolutional Network (TCN) module predicts the landmark quickly but accurately enough as a preliminary, by taking low-resolution version of the detected face holistically as the input. The following Residual Convolutional Networks (RCN) module progressively refines the landmark by taking as input the local patch extracted around the predicted landmark, particularly, which allows the Convolutional Neural Network (CNN) to extract local shape-indexed features to fine tune landmark position. Extensive evaluations show that the proposed Tweaked Residual Convolutional Network approach outperforms existing methods.

Trials and Tribulations of SLA Framework in Designing Arabic Courses for Speakers of Other Languages

ERIC Educational Resources Information Center

Gabsi, Zouhir; Patel, Fay; Hamad, Ahmed

2015-01-01

There is a consensus among language teachers and researchers that language course design is always a work in progress. This is influenced by variables such as the type of language being taught and whether the teaching of this language has been researched. Arabic is one the languages that have created a perennial debate among its teachers about the…

Using Philosophical Liberalism and Philosophical Conservatism as an Organizing Theme in the First Half of the American History Survey

ERIC Educational Resources Information Center

Morris, Richard J.

2009-01-01

Since approximately 1970, many historians have been seeking a unifying theme for the American History Survey. Early in the twentieth century, Progressive historians identified class conflict as the main theme in American History, but during the 1950s and 1960s, this view was challenged by the Consensus Schools' assertion that Americans have always…

Consensus-based approach to develop a measurement framework and identify a core set of indicators to track implementation and progress towards effective coverage of facility-based Kangaroo Mother Care.

PubMed

Guenther, Tanya; Moxon, Sarah; Valsangkar, Bina; Wetzel, Greta; Ruiz, Juan; Kerber, Kate; Blencowe, Hannah; Dube, Queen; Vani, Shashi N; Vivio, Donna; Magge, Hema; De Leon-Mendoza, Socorro; Patterson, Janna; Mazia, Goldy

2017-12-01

As efforts to scale up the delivery of Kangaroo Mother Care (KMC) in facilities are increasing, a standardized approach to measure implementation and progress towards effective coverage is needed. Here, we describe a consensus-based approach to develop a measurement framework and identify a core set of indicators for monitoring facility-based KMC that would be feasible to measure within existing systems. The KMC measurement framework and core list of indicators were developed through: 1) scoping exercise to identify potential indicators through literature review and requests from researchers and program implementers; and 2) face-to-face consultations with KMC and measurement experts working at country and global levels to review candidate indicators and finalize selection and definitions. The KMC measurement framework includes two main components: 1) service readiness, based on the WHO building blocks framework; and 2) service delivery action sequence covering identification, service initiation, continuation to discharge, and follow-up to graduation. Consensus was reached on 10 core indicators for KMC, which were organized according to the measurement framework. We identified 4 service readiness indicators, capturing national level policy for KMC, availability of KMC indicators in HMIS, costed operational plans for KMC and availability of KMC services at health facilities with inpatient maternity services. Six indicators were defined for service delivery, including weighing of babies at birth, identification of those ≤2000 g, initiation of facility-based KMC, monitoring the quality of KMC, status of babies at discharge from the facility and levels of follow-up (according to country-specific protocol). These core KMC indicators, identified with input from a wide range of global and country-level KMC and measurement experts, can aid efforts to strengthen monitoring systems and facilitate global tracking of KMC implementation. As data collection systems advance, we encourage program managers and evaluators to document their experiences using this framework to measure progress and allow indicator refinement, with the overall aim of working towards sustainable, country-led data systems.

Developing Coherent Conceptual Storylines: Two Elementary Challenges

ERIC Educational Resources Information Center

Hanuscin, Deborah; Lipsitz, Kelsey; Cisterna-Alburquerque, Dante; Arnone, Kathryn A.; van Garderen, Delinda; de Araujo, Zandra; Lee, Eun Ju

2016-01-01

The "conceptual storyline" of a lesson refers to the flow and sequencing of learning activities such that science concepts align and progress in ways that are instructionally meaningful to student learning of the concepts. Research demonstrates that when teachers apply lesson design strategies to create a coherent science content…

The Dissociative University: Pragmatist Reconstructions in Democratic Pedagogy

ERIC Educational Resources Information Center

Hachem, Ali H.

2016-01-01

The American university is in transition, witnessing major changes to its institutional structures and processes. While the 1960s and 1970s were decades of progressive democratization in American higher education, today's university is more aligned with the economic theory of neoliberalism. Existing at the intersection of two dominant but…

Culturally grounded indicators of resilience in social-ecological systems

Treesearch

Eleanor Sterling; Tamara Ticktin; Tē Kipa Kepa Morgan; Georgina Cullman; Diana Alvira; Pelika Andrade; Nadia Bergamini; Erin Betley; Kate Burrows; Sophie Caillon; Joachim Claudet; Rachel Dacks; Pablo Eyzaguirre; Chris Filardi; Nadav Gazit; Christian Giardina; Stacy Jupiter; Kealohanuiopuna Kinney; Joe McCarter; Manuel Mejia; Kanoe Morishige; Jennifer Newell; Lihla Noori; John Parks; Pua‘ala Pascua; Ashwin Ravikumar; Jamie Tanguay; Amanda Sigouin; Tina Stege; Mark Stege; Alaka Wali

2017-01-01

Measuring progress toward sustainability goals is a multifaceted task. International, regional, and national organizations and agencies seek to promote resilience and capacity for adaptation at local levels. However, their measurement systems may be poorly aligned with local contexts, cultures, and needs. Understanding how to build effective, culturally grounded...

Forward Thinking. Progress Report, 2010

ERIC Educational Resources Information Center

Colorado Department of Education, 2010

2010-01-01

Since 2007, "Forward Thinking" has provided the roadmap for the department's work. These goals have served the department well in aligning and focusing the work at hand. The goals are: (1) Provide guidance and support to meet school and district needs; (2) Enhance professional development involving best practices; (3) Develop tools to…

Predicting Students' Writing Performance on the NAEP from Student- and State-Level Variables

ERIC Educational Resources Information Center

Mo, Ya; Troia, Gary A.

2017-01-01

This study examines the relationship between students' demographic background and their experiences with writing at school, the alignment between state and National Assessment of Educational Progress (NAEP) direct writing assessments, and students' NAEP writing performance. The study utilizes primary data collection via content analysis of writing…

Early Verb Learning: How Do Children Learn How to Compare Events?

ERIC Educational Resources Information Center

Childers, Jane B.; Parrish, Rebecca; Olson, Christina V.; Burch, Clare; Fung, Gavin; McIntyre, Kevin P.

2016-01-01

An important problem verb learners must solve is how to extend verbs. Children could use cross-situational information to guide their extensions; however, comparing events is difficult. In 2 studies, researchers tested whether children benefit from initially seeing a pair of similar events ("progressive alignment") while learning new…

A large-scale, higher-level, molecular phylogenetic study of the insect order Lepidoptera (moths and butterflies)

USDA-ARS?s Scientific Manuscript database

Higher-level relationships within the Lepidoptera, and particularly within the species-rich subclade Ditrysia, are generally not well understood, although recent studies have yielded progress. 483 taxa spanning 115 of 124 families were sampled for 19 protein-coding nuclear genes. Their aligned nucle...

Peru and its new challenge in higher education: Towards a research university.

PubMed

Lavalle, Carlos; de Nicolas, Victor Luis

2017-01-01

The paradigm of research universities linked to the emergence of university rankings has unified and universalized the criteria relating to the quality of higher education. This situation has led to multiple responses across global society, which has started rating the quality of higher education systems through these rankings, supported by a series of indicators aligned to the characteristics of research universities. Given that the quality of a country's higher education is one of the fundamental pillars of its development, many countries have started to take government action in this respect. In the case of Peru this has not taken long, with the approval of Law 30220 in 2014. This aims to regulate the quality of higher education through a series of specific conditions governed by a newly created body known as SUNEDU. This article uses a Delphi panel to analyze the existing relationship between the conditions imposed by SUNEDU and the research universities' intrinsic characteristics. During the Delphi panel a consensus was reached through an acceptable and stable level of responses, resulting in confirmation that there is alignment between the conditions imposed by SUNEDU and the intrinsic characteristics of research universities.

Peru and its new challenge in higher education: Towards a research university

PubMed Central

2017-01-01

The paradigm of research universities linked to the emergence of university rankings has unified and universalized the criteria relating to the quality of higher education. This situation has led to multiple responses across global society, which has started rating the quality of higher education systems through these rankings, supported by a series of indicators aligned to the characteristics of research universities. Given that the quality of a country’s higher education is one of the fundamental pillars of its development, many countries have started to take government action in this respect. In the case of Peru this has not taken long, with the approval of Law 30220 in 2014. This aims to regulate the quality of higher education through a series of specific conditions governed by a newly created body known as SUNEDU. This article uses a Delphi panel to analyze the existing relationship between the conditions imposed by SUNEDU and the research universities’ intrinsic characteristics. During the Delphi panel a consensus was reached through an acceptable and stable level of responses, resulting in confirmation that there is alignment between the conditions imposed by SUNEDU and the intrinsic characteristics of research universities. PMID:28787463

Selective mutism: a consensus based care pathway of good practice.

PubMed

Keen, D V; Fonseca, S; Wintgens, A

2008-10-01

Selective mutism (SM) now acknowledged as an anxiety condition, tends to be a poorly understood, highly complex and vastly under-recognised clinical entity. Children with SM are a vulnerable group as the condition is not the remit of any one professional group. This inevitably leads to delay in formal diagnosis and management. There is a lack of systematic research on which to base guidelines for management. To develop, agree and validate key principles underlying the management of SM through a consensus process involving international experts, in order to create a local care pathway. A local multi-agency consultation process developed 11 statements, which were felt to be the key principles underpinning a potential care pathway for managing SM. Thirteen recognised experts from North America, Europe and Australia participated in a modified Delphi process involving two rounds using a Likert-scale and free commentary. Both quantitative and qualitative analyses were used in the validation or revision of the statements at each stage. Response rates were 100% for Round 1 and 84.6% for Round 2. Despite the differing professional backgrounds and service contexts, by successive revision and/or revalidation of statements, it was possible to arrive at a consensus about key principles relating to early recognition, assessment and intervention. The agreed key principles are presented together with the resulting local care pathway. Through a Delphi process, agreement was reached by a multidisciplinary group of professionals, on key principles that underpin the timely identification, assessment and management of children with SM. These include the potential for staff in school/preschool settings to identify SM and that intervention programmes should generally be based in these settings. Children with SM should receive assessment for possible coexisting disorders, whether developmental, emotional or behavioural and additional specific intervention given for these. Agreement was reached as to what constitutes clinical progress, intervals for monitoring progress, criteria for referral onwards for multidisciplinary specialist assessment and the role of selective serotonin reuptake inhibitor (SSRI) medication. A consensus methodology has been successfully used to compensate for the lack of evidence base and harness the expertise of a relatively small number of experienced professionals in order to provide a basis for the future development of services.

Severity of spine malalignment on center of pressure progression during level walking in subjects with adolescent idiopathic scoliosis.

PubMed

Chern, Jen-Suh; Kao, Chia-Chi; Lai, Po-Lian; Lung, Chi-Wen; Chen, Wen-Jer

2014-01-01

Center of pressure (CoP) progression during level walking in subjects with Adolescents Idiopathic Scoliosis (AIS) was measured. Participants were divided into three groups according to scoliosis severity. CoP progression among groups was compared quantitatively and qualitatively. The results showed that scoliosis severity affects CoP progression significantly in the hind-foot and forefoot areas. This result indicated that spine alignment might affect the control of heel, ankle and toe rockers in the ankle-foot complex. The effects of scoliosis severity is mainly on the CoP of right foot plantar surface, indicating asymmetrical influence of IS on bilateral lower limb coordination during walking. These results might contribute to musculoskeletal complains over the apparatus within trunk-foot in the later lives of this population.

What Are the Prognostic Factors for Radiographic Progression of Knee Osteoarthritis? A Meta-analysis.

PubMed

Bastick, Alex N; Belo, Janneke N; Runhaar, Jos; Bierma-Zeinstra, Sita M A

2015-09-01

A previous systematic review on prognostic factors for knee osteoarthritis (OA) progression showed associations for generalized OA and hyaluronic acid levels. Knee pain, radiographic severity, sex, quadriceps strength, knee injury, and regular sport activities were not associated. It has been a decade since the literature search of that review and many studies have been performed since then investigating prognostic factors for radiographic knee OA progression. The purpose of this study is to provide an updated systematic review of available evidence regarding prognostic factors for radiographic knee OA progression. We searched for observational studies in MEDLINE and EMBASE. Key words were: knee, osteoarthritis (or arthritis, or arthrosis, or degenerative joint disease), progression (or prognosis, or precipitate, or predictive), and case-control (or cohort, or longitudinal, or follow-up). Studies fulfilling the inclusion criteria were assessed for methodologic quality according to established criteria for reviews on prognostic factors in musculoskeletal disorders. Data were extracted and results were pooled if possible or summarized according to a best-evidence synthesis. A total of 1912 additional articles were identified; 43 met our inclusion criteria. The previous review contained 36 articles, thus providing a new total of 79 articles. Seventy-two of the included articles were scored high quality, the remaining seven were low quality. The pooled odds ratio (OR) of two determinants showed associations with knee OA progression: baseline knee pain (OR, 2.38 [95% CI, 1.74-3.27) and Heberden nodes (OR, 2.66 [95% CI, 1.46-8.84]). Our best-evidence synthesis showed strong evidence that varus alignment, serum hyaluronic acid, and tumor necrosis factor-α are associated with knee OA progression. There is strong evidence that sex, former knee injury, quadriceps strength, smoking, running, and regular performance of sports are not associated with knee OA progression. Evidence for the majority of determined associations, however, was limited, conflicting, or inconclusive. Baseline knee pain, presence of Heberden nodes, varus alignment, and high levels of serum markers hyaluronic acid and tumor necrosis factor-α predict knee OA progression. Sex, knee injury, and quadriceps strength, among others, did not predict knee OA progression. Large variation remains in definitions of knee OA and knee OA progression. Clinical studies should use more consistent definitions of these factors to facilitate data pooling by future meta-analyses.

Reformation of Regulatory Technical Standards for Nuclear Power Generation Equipments in Japan

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

Mikio Kurihara; Masahiro Aoki; Yu Maruyama

2006-07-01

Comprehensive reformation of the regulatory system has been introduced in Japan in order to apply recent technical progress in a timely manner. 'The Technical Standards for Nuclear Power Generation Equipments', known as the Ordinance No.622) of the Ministry of International Trade and Industry, which is used for detailed design, construction and operating stage of Nuclear Power Plants, was being modified to performance specifications with the consensus codes and standards being used as prescriptive specifications, in order to facilitate prompt review of the Ordinance with response to technological innovation. The activities on modification were performed by the Nuclear and Industrial Safetymore » Agency (NISA), the regulatory body in Japan, with support of the Japan Nuclear Energy Safety Organization (JNES), a technical support organization. The revised Ordinance No.62 was issued on July 1, 2005 and is enforced from January 1 2006. During the period from the issuance to the enforcement, JNES carried out to prepare enforceable regulatory guide which complies with each provisions of the Ordinance No.62, and also made technical assessment to endorse the applicability of consensus codes and standards, in response to NISA's request. Some consensus codes and standards were re-assessed since they were already used in regulatory review of the construction plan submitted by licensee. Other consensus codes and standards were newly assessed for endorsement. In case that proper consensus code or standards were not prepared, details of regulatory requirements were described in the regulatory guide as immediate measures. At the same time, appropriate standards developing bodies were requested to prepare those consensus code or standards. Supplementary note which provides background information on the modification, applicable examples etc. was prepared for convenience to the users of the Ordinance No. 62. This paper shows the activities on modification and the results, following the NISA's presentation at ICONE-13 that introduced the framework of the performance specifications and the modification process of the Ordinance NO. 62. (authors)« less

Clinical strategies for the management of intestinal obstruction and pseudo-obstruction. A Delphi Consensus study of SICUT (Società Italiana di Chirurgia d'Urgenza e del Trauma).

PubMed

Costa, Gianluca; Ruscelli, Paolo; Balducci, Genoveffa; Buccoliero, Francesco; Lorenzon, Laura; Frezza, Barbara; Chirletti, Piero; Stagnitti, Franco; Miniello, Stefano; Stella, Francesco

2016-01-01

Intestinal obstructions/pseudo-obstruction of the small/large bowel are frequent conditions but their management could be challenging. Moreover, a general agreement in this field is currently lacking, thus SICUT Society designed a consensus study aimed to define their optimal workout. The Delphi methodology was used to reach consensus among 47 Italian surgical experts in two study rounds. Consensus was defined as an agreement of 75.0% or greater. Four main topic areas included nosology, diagnosis, management and treatment. A bowel obstruction was defined as an obstacle to the progression of intestinal contents and fluids generally beginning with a sudden onset. The panel identified four major criteria of diagnosis including absence of flatus, presence of >3.5 cm ileal levels or >6 cm colon dilatation and abdominal distension. Panel also recommended a surgical admission, a multidisciplinary approach, and a gastrografin swallow for patients presenting occlusions. Criteria for immediate surgery included: presence of strangulated hernia, a >10 cm cecal dilatation, signs of vascular pedicles obstructions and persistence of metabolic acidosis. Moreover, rules for non-operative management (to be conducted for maximum 72 hours) included a naso-gastric drainage placement and clinical and laboratory controls each 12 hours. Non-operative treatment should be suspended if any suspects of intra-abdominal complications, high level of lactates, leukocytosis (>18.000/mm3 or Neutrophils >85%) or a doubling of creatinine level comparing admission. Conversely, consensus was not reached regarding the exact timing of CT scan and the appropriateness of colonic stenting. This consensus is in line with current international strategies and guidelines, and it could be a useful tool in the safe basic daily management of these common and peculiar diseases. Delphi study, Intestinal obstruction, Large bowel obstruction, Pseudo-obstruction, Small bowel.

Design of multiple sequence alignment algorithms on parallel, distributed memory supercomputers.

PubMed

Church, Philip C; Goscinski, Andrzej; Holt, Kathryn; Inouye, Michael; Ghoting, Amol; Makarychev, Konstantin; Reumann, Matthias

2011-01-01

The challenge of comparing two or more genomes that have undergone recombination and substantial amounts of segmental loss and gain has recently been addressed for small numbers of genomes. However, datasets of hundreds of genomes are now common and their sizes will only increase in the future. Multiple sequence alignment of hundreds of genomes remains an intractable problem due to quadratic increases in compute time and memory footprint. To date, most alignment algorithms are designed for commodity clusters without parallelism. Hence, we propose the design of a multiple sequence alignment algorithm on massively parallel, distributed memory supercomputers to enable research into comparative genomics on large data sets. Following the methodology of the sequential progressiveMauve algorithm, we design data structures including sequences and sorted k-mer lists on the IBM Blue Gene/P supercomputer (BG/P). Preliminary results show that we can reduce the memory footprint so that we can potentially align over 250 bacterial genomes on a single BG/P compute node. We verify our results on a dataset of E.coli, Shigella and S.pneumoniae genomes. Our implementation returns results matching those of the original algorithm but in 1/2 the time and with 1/4 the memory footprint for scaffold building. In this study, we have laid the basis for multiple sequence alignment of large-scale datasets on a massively parallel, distributed memory supercomputer, thus enabling comparison of hundreds instead of a few genome sequences within reasonable time.

How we tackled the problem of assessing humanities, social and behavioural sciences in medical education.

PubMed

Goodwin, Dawn; Machin, Laura

2016-01-01

Assessment serves as an important motivation for learning. However, multiple choice and short answer question formats are often considered unsatisfactory for assessment of medical humanities, and the social and behavioural sciences. Little consensus exists as to what might constitute 'best' assessment practice. What we did: We designed an assessment format closely aligned to the curricular approach of problem-based learning which allows for greater assessment of students' understanding, depth of knowledge and interpretation, rather than recall of rote learning. The educational impact of scenario-based assessment has been profound. Students reported changing their approach to PBL, independent learning and exam preparation by taking a less reductionist, more interpretative approach to the topics studied.

Creationism and intelligent design are incompatible with scientific progress: A response to Shanta and Vêdanta.

PubMed

Caetano-Anollés, Gustavo

2016-01-01

In a recent opinion paper, B.K. Shanta claims science leaves no room for the subjective aspect of consciousness, and in doing so, attacks both origin of life and evolutionary research. He claims Vêdanta, one of the 6 orthodox schools of Hindu philosophy, offers an explanation: "the origin of everything material and nonmaterial is sentient and absolute." Here I discuss how the pseudoscience of these creationist views, which are aligned with Intelligent Design, are incompatible with scientific progress and should not be published in scientific journals.

Updated consensus statement on the use of rituximab in patients with rheumatoid arthritis

PubMed Central

Buch, Maya H; Smolen, Josef S; Betteridge, Neil; Breedveld, Ferdinand C; Burmester, Gerd; Dörner, Thomas; Ferraccioli, Gianfranco; Gottenberg, Jacques-Eric; Isaacs, John; Kvien, Tore K; Mariette, Xavier; Martin-Mola, Emilio; Pavelka, Karel; Tak, Paul P; van der Heijde, Desiree; van Vollenhoven, Ronald F; Emery, Paul

2011-01-01

Background Since initial approval for the treatment of rheumatoid arthritis (RA), rituximab has been evaluated in clinical trials involving various populations with RA. Information has also been gathered from registries. This report therefore updates the 2007 consensus document on the use of rituximab in the treatment of RA. Methods Preparation of this new document involved many international experts experienced in the treatment of RA. Following a meeting to agree upon the core agenda, a systematic literature review was undertaken to identify all relevant data. Data were then interrogated by a drafting committee, with subsequent review and discussion by a wider expert committee leading to the formulation of an updated consensus statement. These committees also included patients with RA. Results The new statement covers wide-ranging issues including the use of rituximab in earlier RA and impact on structural progression, and aspects particularly pertinent to rituximab such as co-medication, optimal dosage regimens, repeat treatment cycles and how to manage non-response. Biological therapy following rituximab usage is also addressed, and safety concerns including appropriate screening for hepatitis, immunoglobulin levels and infection risk. This consensus statement will support clinicians and inform patients when using B-cell depletion in the management of RA, providing up-to-date information and highlighting areas for further research. Conclusion New therapeutic strategies and treatment options for RA, a chronic destructive and disabling disease, have expanded over recent years. These have been summarised in general strategic suggestions and specific management recommendations, emphasising the importance of expedient disease-modifying antirheumatic drug implementation and tight disease control. This consensus statement is in line with these fundamental principles of management. PMID:21378402

Consensus on Quality Indicators of Postgraduate Medical E-Learning: Delphi Study.

PubMed

de Leeuw, Robert Adrianus; Walsh, Kieran; Westerman, Michiel; Scheele, Fedde

2018-04-26

The progressive use of e-learning in postgraduate medical education calls for useful quality indicators. Many evaluation tools exist. However, these are diversely used and their empirical foundation is often lacking. We aimed to identify an empirically founded set of quality indicators to set the bar for “good enough” e-learning. We performed a Delphi procedure with a group of 13 international education experts and 10 experienced users of e-learning. The questionnaire started with 57 items. These items were the result of a previous literature review and focus group study performed with experts and users. Consensus was met when a rate of agreement of more than two-thirds was achieved. In the first round, the participants accepted 37 items of the 57 as important, reached no consensus on 20, and added 15 new items. In the second round, we added the comments from the first round to the items on which there was no consensus and added the 15 new items. After this round, a total of 72 items were addressed and, of these, 37 items were accepted and 34 were rejected due to lack of consensus. This study produced a list of 37 items that can form the basis of an evaluation tool to evaluate postgraduate medical e-learning. This is, to our knowledge, the first time that quality indicators for postgraduate medical e-learning have been defined and validated. The next step is to create and validate an e-learning evaluation tool from these items. ©Robert Adrianus de Leeuw, Kieran Walsh, Michiel Westerman, Fedde Scheele. Originally published in JMIR Medical Education (http://mededu.jmir.org), 26.04.2018.

Expert consensus for performing right heart catheterisation for suspected pulmonary arterial hypertension in systemic sclerosis: a Delphi consensus study with cluster analysis.

PubMed

Avouac, Jérôme; Huscher, Dörte; Furst, Daniel E; Opitz, Christian F; Distler, Oliver; Allanore, Yannick

2014-01-01

To establish an expert consensus on which criteria are the most appropriate in clinical practice to refer patients with systemic sclerosis (SSc) for right heart catheterisation (RHC) when pulmonary hypertension (PH) is suspected. A three stage internet based Delphi consensus exercise involving worldwide PH experts was designed. In the first stage, a comprehensive list of domains and items combining evidence based indications and expert opinions were obtained. In the second and third stages, experts were asked to rate each item selected in the list. After each of stages 2 and 3, the number of items and criteria were reduced according to a cluster analysis. A literature search and the opinions of 47 experts participating in Delphi stage 1 provided a list of seven domains containing 142 criteria. After stages 2 and 3, these domains and tools were reduced to three domains containing eight tools: clinical (progressive dyspnoea over the past 3 months, unexplained dyspnoea, worsening of WHO dyspnoea functional class, any finding on physical examination suggestive of elevated right heart pressures and any sign of right heart failure), echocardiography (systolic pulmonary artery pressure >45 mm Hg and right ventricle dilation) and pulmonary function tests (diffusion lung capacity for carbon monoxide <50% without pulmonary fibrosis). Among experts in pulmonary arterial hypertension-SSc, a core set of criteria for clinical practice to refer SSc patients for RHC has been defined by Delphi consensus methods. Although these indications are recommended by this expert group to be used as an interim tool, it will be necessary to formally validate the present tools in further studies.

KinView: A visual comparative sequence analysis tool for integrated kinome research

PubMed Central

McSkimming, Daniel Ian; Dastgheib, Shima; Baffi, Timothy R.; Byrne, Dominic P.; Ferries, Samantha; Scott, Steven Thomas; Newton, Alexandra C.; Eyers, Claire E.; Kochut, Krzysztof J.; Eyers, Patrick A.

2017-01-01

Multiple sequence alignments (MSAs) are a fundamental analysis tool used throughout biology to investigate relationships between protein sequence, structure, function, evolutionary history, and patterns of disease-associated variants. However, their widespread application in systems biology research is currently hindered by the lack of user-friendly tools to simultaneously visualize, manipulate and query the information conceptualized in large sequence alignments, and the challenges in integrating MSAs with multiple orthogonal data such as cancer variants and post-translational modifications, which are often stored in heterogeneous data sources and formats. Here, we present the Multiple Sequence Alignment Ontology (MSAOnt), which represents a profile or consensus alignment in an ontological format. Subsets of the alignment are easily selected through the SPARQL Protocol and RDF Query Language for downstream statistical analysis or visualization. We have also created the Kinome Viewer (KinView), an interactive integrative visualization that places eukaryotic protein kinase cancer variants in the context of natural sequence variation and experimentally determined post-translational modifications, which play central roles in the regulation of cellular signaling pathways. Using KinView, we identified differential phosphorylation patterns between tyrosine and serine/threonine kinases in the activation segment, a major kinase regulatory region that is often mutated in proliferative diseases. We discuss cancer variants that disrupt phosphorylation sites in the activation segment, and show how KinView can be used as a comparative tool to identify differences and similarities in natural variation, cancer variants and post-translational modifications between kinase groups, families and subfamilies. Based on KinView comparisons, we identify and experimentally characterize a regulatory tyrosine (Y177PLK4) in the PLK4 C-terminal activation segment region termed the P+1 loop. To further demonstrate the application of KinView in hypothesis generation and testing, we formulate and validate a hypothesis explaining a novel predicted loss-of-function variant (D523NPKCβ) in the regulatory spine of PKCβ, a recently identified tumor suppressor kinase. KinView provides a novel, extensible interface for performing comparative analyses between subsets of kinases and for integrating multiple types of residue specific annotations in user friendly formats. PMID:27731453

Visualizing phylogenetic tree landscapes.

PubMed

Wilgenbusch, James C; Huang, Wen; Gallivan, Kyle A

2017-02-02

Genomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes, codon positions, and structural features) often favor hundreds if not thousands of competing phylogenies. Summarizing and comparing phylogenies obtained from multi-source data sets using current consensus tree methods discards valuable information and can disguise potential methodological problems. Discovery of efficient and accurate dimensionality reduction methods used to display at once in 2- or 3- dimensions the relationship among these competing phylogenies will help practitioners diagnose the limits of current evolutionary models and potential problems with phylogenetic reconstruction methods when analyzing large multi-source data sets. We introduce several dimensionality reduction methods to visualize in 2- and 3-dimensions the relationship among competing phylogenies obtained from gene partitions found in three mid- to large-size mitochondrial genome alignments. We test the performance of these dimensionality reduction methods by applying several goodness-of-fit measures. The intrinsic dimensionality of each data set is also estimated to determine whether projections in 2- and 3-dimensions can be expected to reveal meaningful relationships among trees from different data partitions. Several new approaches to aid in the comparison of different phylogenetic landscapes are presented. Curvilinear Components Analysis (CCA) and a stochastic gradient decent (SGD) optimization method give the best representation of the original tree-to-tree distance matrix for each of the three- mitochondrial genome alignments and greatly outperformed the method currently used to visualize tree landscapes. The CCA + SGD method converged at least as fast as previously applied methods for visualizing tree landscapes. We demonstrate for all three mtDNA alignments that 3D projections significantly increase the fit between the tree-to-tree distances and can facilitate the interpretation of the relationship among phylogenetic trees. We demonstrate that the choice of dimensionality reduction method can significantly influence the spatial relationship among a large set of competing phylogenetic trees. We highlight the importance of selecting a dimensionality reduction method to visualize large multi-locus phylogenetic landscapes and demonstrate that 3D projections of mitochondrial tree landscapes better capture the relationship among the trees being compared.

Diagnosis and management of non-alcoholic fatty liver disease and related metabolic disorders: Consensus statement from the Study Group of Liver and Metabolism, Chinese Society of Endocrinology

PubMed Central

Gao, Xin; Fan, Jian-Gao

2013-01-01

Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease in Western countries, affecting 20%–33% of the general population. Large population-based surveys in China indicate a prevalence of approximately 15%–30%. Worldwide, including in China, the prevalence of NAFLD has increased rapidly in parallel with regional trends of obesity, type2 diabetes and metabolic syndrome. In addition, NAFLD has contributed significantly to increased overall, as well as cardiovascular and liver-related, mortality in the general population. In view of rapid advances in research into NAFLD in recent years, this consensus statement provides a brief update on the progress in the field and suggests preferred approaches for the comprehensive management of NAFLD and its related metabolic diseases. PMID:23560695

Identification of adverse events in ground transport emergency medical services.

PubMed

Patterson, P Daniel; Weaver, Matthew D; Abebe, Kaleab; Martin-Gill, Chris; Roth, Ronald N; Suyama, Joseph; Guyette, Francis X; Rittenberger, Jon C; Krackhardt, David; Arnold, Robert; Yealy, Donald M; Lave, Judith

2012-01-01

The purpose of this study was to develop a method to define and rate the severity of adverse events (AEs) in emergency medical services (EMS) safety research. They used a modified Delphi technique to develop a consensus definition of an AE. The consensus definition was as follows: "An adverse event in EMS is a harmful or potentially harmful event occurring during the continuum of EMS care that is potentially preventable and thus independent of the progression of the patient's condition." Physicians reviewed 250 charts from 3 EMS agencies for AEs. The authors examined physician agreement using κ, Fleiss's κ, and corresponding 95% confidence intervals (CIs). Overall physician agreement on presence of an AE per chart was fair (κ = 0.24; 95% CI = 0.19, 0.29). These findings should serve as a basis for refining and implementing an AE evaluation instrument.

Accurate RNA consensus sequencing for high-fidelity detection of transcriptional mutagenesis-induced epimutations.

PubMed

Reid-Bayliss, Kate S; Loeb, Lawrence A

2017-08-29

Transcriptional mutagenesis (TM) due to misincorporation during RNA transcription can result in mutant RNAs, or epimutations, that generate proteins with altered properties. TM has long been hypothesized to play a role in aging, cancer, and viral and bacterial evolution. However, inadequate methodologies have limited progress in elucidating a causal association. We present a high-throughput, highly accurate RNA sequencing method to measure epimutations with single-molecule sensitivity. Accurate RNA consensus sequencing (ARC-seq) uniquely combines RNA barcoding and generation of multiple cDNA copies per RNA molecule to eliminate errors introduced during cDNA synthesis, PCR, and sequencing. The stringency of ARC-seq can be scaled to accommodate the quality of input RNAs. We apply ARC-seq to directly assess transcriptome-wide epimutations resulting from RNA polymerase mutants and oxidative stress.

Is physical exercise a multiple sclerosis disease modifying treatment?

PubMed

Motl, Robert W; Pilutti, Lara A

2016-08-01

There is consensus that exercise represents a behavioral approach for the restoration of function and management of symptoms among persons with multiple sclerosis (MS). The current paper provides a review on the topic of exercise and physical activity as MS-disease modifying treatments. Firstly, metrics for evaluating disease modification and progression in MS are described. Secondly, evidence for exercise as a MS-disease modifying therapy based on individual studies, literature reviews, and meta-analyses is summarized. Finally, the paper focuses on major limitations of the existing body of research. Expert commentary: Exercise and physical activity have been associated with reduced relapse rate, mobility disability and its progression, and lesion volume, and improved neuroperformance, particularly walking outcomes. This evidence provides a positive, yet preliminary, picture for exercise having possible effects on markers of disease modification and progression in MS.

Environment-dependent striatal gene expression in the BACHD rat model for Huntington disease.

PubMed

Novati, Arianna; Hentrich, Thomas; Wassouf, Zinah; Weber, Jonasz J; Yu-Taeger, Libo; Déglon, Nicole; Nguyen, Huu Phuc; Schulze-Hentrich, Julia M

2018-04-11

Huntington disease (HD) is an autosomal dominant neurodegenerative disorder caused by a mutation in the huntingtin (HTT) gene which results in progressive neurodegeneration in the striatum, cortex, and eventually most brain areas. Despite being a monogenic disorder, environmental factors influence HD characteristics. Both human and mouse studies suggest that mutant HTT (mHTT) leads to gene expression changes that harbor potential to be modulated by the environment. Yet, the underlying mechanisms integrating environmental cues into the gene regulatory program have remained largely unclear. To better understand gene-environment interactions in the context of mHTT, we employed RNA-seq to examine effects of maternal separation (MS) and environmental enrichment (EE) on striatal gene expression during development of BACHD rats. We integrated our results with striatal consensus modules defined on HTT-CAG length and age-dependent co-expression gene networks to relate the environmental factors with disease progression. While mHTT was the main determinant of expression changes, both MS and EE were capable of modulating these disturbances, resulting in distinctive and in several cases opposing effects of MS and EE on consensus modules. This bivalent response to maternal separation and environmental enrichment may aid in explaining their distinct effects observed on disease phenotypes in animal models of HD and related neurodegenerative disorders.

Cultural Adaptations of Behavioral Health Interventions: A Progress Report

PubMed Central

Barrera, Manuel

2014-01-01

Objective To reduce health disparities, behavioral health interventions must reach subcultural groups and demonstrate effectiveness in improving their health behaviors and outcomes. One approach to developing such health interventions is to culturally adapt original evidence-based interventions. The goals of the paper are to (a) describe consensus on the stages involved in developing cultural adaptations, (b) identify common elements in cultural adaptations, (c) examine evidence on the effectiveness of culturally enhanced interventions for various health conditions, and (d) pose questions for future research. Method Influential literature from the past decade was examined to identify points of consensus. Results There is agreement that cultural adaptation can be organized into five stages: information gathering, preliminary design, preliminary testing, refinement, and final trial. With few exceptions, reviews of several health conditions (e.g., AIDS, asthma, diabetes) concluded that culturally enhanced interventions are more effective in improving health outcomes than usual care or other control conditions. Conclusion Progress has been made in establishing methods for conducting cultural adaptations and providing evidence of their effectiveness. Future research should include evaluations of cultural adaptations developed in stages, tests to determine the effectiveness of cultural adaptations relative to the original versions, and studies that advance our understanding of cultural constructs’ contributions to intervention engagement and efficacy. PMID:22289132

The Vatican at the United Nations. Cairo + 5.

PubMed

Kissling, F

1999-01-01

During the International Conference on Population and Development in Cairo, a remarkable consensus on population and development was forged and a Programme of Action was issued. With its permanent observer status among governments at the UN, the Vatican had attempted to block such a worldwide consensus on a new structure for population and development programs, based on women's empowerment, universal and voluntary access to contraception, and improved reproductive health for all. After 5 years of implementing the Cairo Programme of Action, the UN conducted a review and appraisal of its implementation, ending with a final preparatory meeting and a Special Session of the UN General Assembly. During the review process and the meeting, the Vatican remained active but fell short, on the whole, of thwarting progress. The Vatican delegation was made up of five individuals--two women and three men, including two priests. Almost all their interventions were focused on the goal of obstructing progressive understanding of what would be necessary if the Programme of Action were to be fully and fairly implemented. This included the provision of emergency contraception to refugees; the definition of human rights; addressing unsafe abortion as a major public health issue; the provision of condoms for protection against HIV/AIDS; adolescent rights to privacy and confidentiality; and the inclusion of sex education in school curricula.

The Mouse Model of Pancreatic Cancer Atlas (MMPCA) for classification of pancreatic cancer lesions: A large histological investigation of the Ptf1aCre/+;LSL-KrasG12D/+ transgenic mouse model of pancreatic cancer

PubMed Central

Veite-Schmahl, Michelle J.; Rivers, Adam C.; Regan, Daniel P.

2017-01-01

Pancreatic ductal adenocarcinoma (PDAC) is one of the leading forms of cancer related deaths in the United States. With limited treatment options and unreliable diagnostic methods, long-term survival rates following a diagnosis of pancreatic cancer remain poor. Pancreatic intraepithelial neoplasia (PanIN) are precancerous lesions that precede progression towards PDAC. PanIN occur in increasing complexity as the disease progresses and the description of PanIN plays a critical role in describing, staging and diagnosing PDAC. Inconsistencies in PanIN classifications exist even amongst leading pathologists. This has led to debate and confusion among researchers and pathologists involved in pancreatic cancer research, diagnosis and treatment. We have sought to initiate a discussion with leading pathologists with a goal of increasing consensus in the interpretation of PanIN and associated structures within the precancerous pancreas. Toward achieving this goal, we are in the process of conducting an extensive study of over 1000 male and female pancreata in varying stages of PanIN progression isolated from the Ptf1aCre/+;LSL-KrasG12D/+ transgenic mouse model of pancreatic cancer. Using this extensive database, we have established the Mouse Model of Pancreatic Cancer Atlas (MMPCA) to serve as a platform for meaningful and interactive discussion among researchers and pathologists who study pancreatic disease. We hope that the MMPCA will be an effective tool for promoting a more consistent and accurate consensus of PanIN classifications in the future. PMID:29121082

Consensus on the diagnosis, treatment and follow-up of patients with Duchenne muscular dystrophy.

PubMed

Nascimento Osorio, A; Medina Cantillo, J; Camacho Salas, A; Madruga Garrido, M; Vilchez Padilla, J J

2018-03-09

Duchenne muscular dystrophy (DMD) is the most common myopathy in children, with a worldwide prevalence of approximately 0.5 cases per 10,000 male births. It is characterised by a progressive muscular weakness manifesting in early childhood, with the subsequent appearance of musculoskeletal, respiratory, and cardiac complications, causing disability, dependence, and premature death. Currently, DMD is mainly managed with multidisciplinary symptomatic treatment, with favourable results in terms of the progression of the disease. It is therefore crucial to establish clear, up-to-date guidelines enabling early detection, appropriate treatment, and monitoring of possible complications. We performed a literature search of the main biomedical databases for articles published in the last 10years in order to obtain an overview of the issues addressed by current guidelines and to identify relevant issues for which no consensus has yet been established. The degree of evidence and level of recommendation of the information obtained were classified and ordered according to the criteria of the American Academy of Neurology. DMD management should be multidisciplinary and adapted to the patient's profile and the stage of clinical progression. In addition to corticotherapy, treatment targeting gastrointestinal, respiratory, cardiac, and orthopaedic problems, as well as physiotherapy, should be provided with a view to improving patients' quality of life. Genetic studies play a key role in the management of the disease, both in detecting cases and potential carriers and in characterising the mutation involved and developing new therapies. Copyright © 2018 Sociedad Española de Neurología. Publicado por Elsevier España, S.L.U. All rights reserved.

Consensus recommendations on the use of daylight photodynamic therapy with methyl aminolevulinate cream for actinic keratoses in Australia

PubMed Central

Shumack, Stephen; Murrell, Dedee F; Rubel, Diana M; Fernández‐Peñas, Pablo; Salmon, Robert; Hewitt, Daniel; Foley, Peter; Spelman, Lynda

2015-01-01

Abstract Australia has the highest prevalence of actinic keratoses (AK) worldwide. Because of the risk of transformation of AK to invasive squamous cell carcinomas, consensus guidelines recommend that AK are removed using appropriate therapies to prevent progression to invasive disease. Daylight photodynamic therapy (PDT) is emerging as an efficacious treatment for AK, particularly for patients who require treatment of large areas of chronic actinic damage that can be exposed easily to daylight. Daylight PDT with methyl aminolevulinate (MAL) cream is a simple treatment for AK, almost painless, well tolerated and convenient, requiring minimal time in the clinic. Randomised controlled studies from northern Europe and Australia support the use of daylight PDT as an effective therapy for grade I and II AK on the face and scalp. There is sufficient daylight to conduct daylight PDT in Australia at any time of the year and during most weather conditions. Hence, daylight PDT with MAL can be included as an effective and well‐tolerated new treatment option for the treatment of AK in Australia. These consensus recommendations provide guidelines for Australian clinicians on the use of daylight PDT in the treatment of diagnosed AK. PMID:26033230

Expert consensus document: Consensus statement on best practice management regarding the use of intravesical immunotherapy with BCG for bladder cancer.

PubMed

Kamat, Ashish M; Flaig, Thomas W; Grossman, H Barton; Konety, Badrinath; Lamm, Donald; O'Donnell, Michael A; Uchio, Edward; Efstathiou, Jason A; Taylor, John A

2015-04-01

Multiple clinical trials have demonstrated that intravesical Bacillus Calmette-Guérin (BCG) treatment reduces recurrences and progression in patients with non-muscle-invasive bladder cancer (NMIBC). However, although BCG has been in use for almost 40 years, this agent is often underutilized and practice patterns of administration vary. This neglect is most likely caused by uncertainties about the optimal use of BCG, including unawareness of optimal treatment schedules and about patient populations that most benefit from BCG treatment. To address this deficit, a focus group of specialized urologic oncologists (urologists, medical oncologists and radiation oncologists) reviewed the current guidelines and clinical evidence, discussed their experiences and formed a consensus regarding the optimal use of BCG in the management of patients with NIMBC. The experts concluded that continuing therapy with 3-week BCG maintenance is superior to induction treatment only and is the single most important factor in improving outcomes in patients with NMIBC. They also concluded that a reliable alternative to radical cystectomy in truly BCG-refractory disease remains the subject of clinical trials. In addition, definitions for common terms of BCG failure, such as BCG-refractory and BCG-intolerant, have been formulated.

Participating in Authentic Science with the Aid of Learning Progressions through Mission Earth Workshops

NASA Astrophysics Data System (ADS)

Lewis, P. M., Jr.; Taylor, J.; Harte, T.; Czajkowski, K. P.

2016-12-01

"MISSION EARTH: Fusing GLOBE with NASA Assets to Build Systemic Innovation In STEM Education" is one of the new education cooperative agreements funded by the NASA Science Mission Directorate. Students will learn how to conduct "real science" through hands-on data collection using Global Learning and Observations to Benefit the Environment (GLOBE) protocols combined with other NASA science educational materials. This project aims to work with educators spanning the full K-12 range, requiring three grade bands of learning progressions and vertical alignment among materials and resources to best meet classroom needs. From K to 12 students have vastly different abilities to conduct and learn from scientific investigations. Hand-picked NASA assets will provide appropriate exposure across the curriculum and grade bands, and we are developing unique learning progressions that bring together GLOBE protocols for data collection and learning activities, NASA data sets through MY NASA DATA for data comparison, and more. The individual materials are not limited to science, but also include all elements of STEM with literacy components added in where appropriate. This will give the students an opportunity to work on better understanding the world around them in a well-rounded way, and offer cross-subject/classroom exposure to improve student understanding. To ensure that these learning progressions can continue to be used in the classroom in the future, alignment to the Next Generation Science Standards will help frame all of the materials and products. The learning progressions will be living documents that will change based on context. After several iterations, it is our goal to produce learning progressions for grades K-12 that will allow any STEM teacher to pick up and infuse NASA and GLOBE in their classroom at any location and at any time in their school year. This presentation will share results from the first year of development for this project.

Genetic algorithms for protein threading.

PubMed

Yadgari, J; Amir, A; Unger, R

1998-01-01

Despite many years of efforts, a direct prediction of protein structure from sequence is still not possible. As a result, in the last few years researchers have started to address the "inverse folding problem": Identifying and aligning a sequence to the fold with which it is most compatible, a process known as "threading". In two meetings in which protein folding predictions were objectively evaluated, it became clear that threading as a concept promises a real breakthrough, but that much improvement is still needed in the technique itself. Threading is a NP-hard problem, and thus no general polynomial solution can be expected. Still a practical approach with demonstrated ability to find optimal solutions in many cases, and acceptable solutions in other cases, is needed. We applied the technique of Genetic Algorithms in order to significantly improve the ability of threading algorithms to find the optimal alignment of a sequence to a structure, i.e. the alignment with the minimum free energy. A major progress reported here is the design of a representation of the threading alignment as a string of fixed length. With this representation validation of alignments and genetic operators are effectively implemented. Appropriate data structure and parameters have been selected. It is shown that Genetic Algorithm threading is effective and is able to find the optimal alignment in a few test cases. Furthermore, the described algorithm is shown to perform well even without pre-definition of core elements. Existing threading methods are dependent on such constraints to make their calculations feasible. But the concept of core elements is inherently arbitrary and should be avoided if possible. While a rigorous proof is hard to submit yet an, we present indications that indeed Genetic Algorithm threading is capable of finding consistently good solutions of full alignments in search spaces of size up to 10(70).

Gathering Requirements for Teacher Tools: Strategies for Empowering Teachers through Co-Design

ERIC Educational Resources Information Center

Matuk, Camillia; Gerard, Libby; Lim-Breitbart, Jonathan; Linn, Marcia

2016-01-01

Technology can enhance teachers' practice in multiple ways. It can help them better understand patterns in their students' thinking, manage class progress at individual and group levels, and obtain evidence to inform modifications to curriculum and instruction. Such technology is most effective when it is aligned with teachers' goals and…

"Our Door Is Always Open": Aligning Literacy Learning Practices in Writing Programs and Residential Learning Communities

ERIC Educational Resources Information Center

Voss, Julia

2016-01-01

Writing studies has considered college students' literacy development as a chronological progression and as influenced by their off-campus connections to various cultural and professional communities. This project considers students' literacy development across disciplines and university activity systems in which they're simultaneously involved to…

PK-3: What Does It Mean for Instruction? Social Policy Report. Volume 30, Number 2

ERIC Educational Resources Information Center

Stipek, Deborah; Franke, Megan; Clements, Doug; Farran, Dale; Coburn, Cynthia

2017-01-01

"PK--3" has become a rallying cry among many developmental scientists and educators. A central component of this movement is alignment between preschool and the early elementary grades. Many districts have made policy changes designed to promote continuity in children's educational experiences as they progress from preschool through…

Crucial Issues in California Education 2006: Rekindling Reform

ERIC Educational Resources Information Center

Hass, Bob, Ed.

2006-01-01

Educators and policymakers have accomplished much over the past decade, aided by parents and taxpayers. California has set a high bar for what all children are expected to learn, from kindergarten forward. Instructional materials and tests are now closely aligned, so that teachers know how to gauge their students' progress. And achievement growth…

Illusory Liberalism in "Atlas de Geografía Humana"

ERIC Educational Resources Information Center

Ryan, Lorraine

2014-01-01

"Atlas de Geografía Humana" constitutes a critique of the much vaunted notion of a progressive Spain that has rectified the gender inequalities of the Francoist era, as one of the highly educated and successful protagonists, Fran, unwittingly adopts her mother's alignment with patriarchal norms. This novel elucidates the incompatibility…

Multi-port valve assembly

DOEpatents

Guggenheim, S. Frederic

1986-01-01

A multi-port fluid valve apparatus is used to control the flow of fluids through a plurality of valves and includes a web, which preferably is a stainless steel endless belt. The belt has an aperture therethrough and is progressed, under motor drive and control, so that its aperture is moved from one valve mechanism to another. Each of the valve mechanisms comprises a pair of valve blocks which are held in fluid-tight relationship against the belt. Each valve block consists of a block having a bore through which the fluid flows, a first seal surrounding the bore and a second seal surrounding the first seal, with the distance between the first and second seals being greater than the size of the belt aperture. In order to open a valve, the motor progresses the belt aperture to where it is aligned with the two bores of a pair of valve blocks, such alignment permitting a flow of the fluid through the valve. The valve is closed by movement of the belt aperture and its replacement, within the pair of valve blocks, by a solid portion of the belt.

Ultrasound monitoring of inter-knee distances during gait.

PubMed

Lai, Daniel T H; Wrigley, Tim V; Palaniswami, M

2009-01-01

Knee osteoarthritis is an extremely common, debilitating disease associated with pain and loss of function. There is considerable interest in monitoring lower limb alignment due to its close association with joint overload leading to disease progression. The effects of gait modifications that can lower joint loading are of particular interest. Here we describe an ultrasound-based system for monitoring an important aspect of dynamic lower limb alignment, the inter-knee distance during walking. Monitoring this gait parameter should facilitate studies in reducing knee loading, a primary risk factor of knee osteoarthritis progression. The portable device is composed of an ultrasound sensor connected to an Intel iMote2 equipped with Bluetooth wireless capability. Static tests and calibration results show that the sensor possesses an effective beam envelope of 120 degrees, with maximum distance errors of 10% at the envelope edges. Dynamic walking trials reveal close correlation of inter-knee distance trends between that measured by an optical system (Optotrak Certus NDI) and the sensor device. The maximum average root mean square error was found to be 1.46 cm. Future work will focus on improving the accuracy of the device.

Tree decomposition based fast search of RNA structures including pseudoknots in genomes.

PubMed

Song, Yinglei; Liu, Chunmei; Malmberg, Russell; Pan, Fangfang; Cai, Liming

2005-01-01

Searching genomes for RNA secondary structure with computational methods has become an important approach to the annotation of non-coding RNAs. However, due to the lack of efficient algorithms for accurate RNA structure-sequence alignment, computer programs capable of fast and effectively searching genomes for RNA secondary structures have not been available. In this paper, a novel RNA structure profiling model is introduced based on the notion of a conformational graph to specify the consensus structure of an RNA family. Tree decomposition yields a small tree width t for such conformation graphs (e.g., t = 2 for stem loops and only a slight increase for pseudo-knots). Within this modelling framework, the optimal alignment of a sequence to the structure model corresponds to finding a maximum valued isomorphic subgraph and consequently can be accomplished through dynamic programming on the tree decomposition of the conformational graph in time O(k(t)N(2)), where k is a small parameter; and N is the size of the projiled RNA structure. Experiments show that the application of the alignment algorithm to search in genomes yields the same search accuracy as methods based on a Covariance model with a significant reduction in computation time. In particular; very accurate searches of tmRNAs in bacteria genomes and of telomerase RNAs in yeast genomes can be accomplished in days, as opposed to months required by other methods. The tree decomposition based searching tool is free upon request and can be downloaded at our site h t t p ://w.uga.edu/RNA-informatics/software/index.php.

Reference-guided assembly of four diverse Arabidopsis thaliana genomes

PubMed Central

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

2011-01-01

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

A survey of the Cape Floristic Region of South Africa for the presence of cyst nematodes (Nematoda: Heteroderidae).

PubMed

Knoetze, Rinus; Swart, Antoinette

2014-12-09

A survey was performed to detect the presence of cyst nematodes in the Cape Floristic Region of South Africa. Soil was collected in the rhizosphere of the dominant plant species within blocks of indigenous vegetation and cysts were extracted from them. A total of 81 blocks of indigenous vegetation were sampled as described. Cysts were detected in 7 of these samples, representing 6 different vegetation types. One set of primers was used to amplify the ITS regions from these cysts, including the 5.8S ribosomal gene, as well as short parts of the 18S and 28S ribosomal genes. ITS-rDNA sequences from the indigenous isolates were aligned with selected sequences of other species from the Heteroderidae. Phylogenetic analyses to resolve the relationships between indigenous isolates and selected representatives of the Heteroderidae were conducted using the Maximum Parsimony method. The consensus tree resulting from alignment of the circumfenestrate cysts revealed that isolates SK18, WK1 and WK26 are included in a clade of Globodera species that parasitise non-solanaceous plants, forming a monophyletic group with G. millefolii, G. artemisiae, and an unidentified Globodera sp. from Portugal. In a tree resulting from the alignment of the Heterodera spp., isolates OK14 and WK2 are included in the Afenestrata group, forming a monophyletic group with H. orientalis.This survey unearthed at least four potentially new species of cyst nematodes, which may prove invaluable for the study of the evolution and biogeography of the group.

The influence of ignoring secondary structure on divergence time estimates from ribosomal RNA genes.

PubMed

Dohrmann, Martin

2014-02-01

Genes coding for ribosomal RNA molecules (rDNA) are among the most popular markers in molecular phylogenetics and evolution. However, coevolution of sites that code for pairing regions (stems) in the RNA secondary structure can make it challenging to obtain accurate results from such loci. While the influence of ignoring secondary structure on multiple sequence alignment and tree topology has been investigated in numerous studies, its effect on molecular divergence time estimates is still poorly known. Here, I investigate this issue in Bayesian Markov Chain Monte Carlo (BMCMC) and penalized likelihood (PL) frameworks, using empirical datasets from dragonflies (Odonata: Anisoptera) and glass sponges (Porifera: Hexactinellida). My results indicate that highly biased inferences under substitution models that ignore secondary structure only occur if maximum-likelihood estimates of branch lengths are used as input to PL dating, whereas in a BMCMC framework and in PL dating based on Bayesian consensus branch lengths, the effect is far less severe. I conclude that accounting for coevolution of paired sites in molecular dating studies is not as important as previously suggested, as long as the estimates are based on Bayesian consensus branch lengths instead of ML point estimates. This finding is especially relevant for studies where computational limitations do not allow the use of secondary-structure specific substitution models, or where accurate consensus structures cannot be predicted. I also found that the magnitude and direction (over- vs. underestimating node ages) of bias in age estimates when secondary structure is ignored was not distributed randomly across the nodes of the phylogenies, a phenomenon that requires further investigation. Copyright © 2013 Elsevier Inc. All rights reserved.

Evaluation of Changes in Morphology and Function of Human Induced Pluripotent Stem Cell Derived Cardiomyocytes (HiPSC-CMs) Cultured on an Aligned-Nanofiber Cardiac Patch

PubMed Central

Khan, Mahmood; Xu, Yanyi; Hua, Serena; Johnson, Jed; Belevych, Andriy; Janssen, Paul M. L.; Gyorke, Sandor; Guan, Jianjun; Angelos, Mark G.

2015-01-01

Introduction Dilated cardiomyopathy is a major cause of progressive heart failure. Utilization of stem cell therapy offers a potential means of regenerating viable cardiac tissue. However, a major obstacle to stem cell therapy is the delivery and survival of implanted stem cells in the ischemic heart. To address this issue, we have developed a biomimetic aligned nanofibrous cardiac patch and characterized the alignment and function of human inducible pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) cultured on this cardiac patch. This hiPSC-CMs seeded patch was compared with hiPSC-CMs cultured on standard flat cell culture plates. Methods hiPSC-CMs were cultured on; 1) a highly aligned polylactide-co-glycolide (PLGA) nanofiber scaffold (~50 microns thick) and 2) on a standard flat culture plate. Scanning electron microscopy (SEM) was used to determine alignment of PLGA nanofibers and orientation of the cells on the respective surfaces. Analysis of gap junctions (Connexin-43) was performed by confocal imaging in both the groups. Calcium cycling and patch-clamp technique were performed to measure calcium transients and electrical coupling properties of cardiomyocytes. Results SEM demonstrated >90% alignment of the nanofibers in the patch which is similar to the extracellular matrix of decellularized rat myocardium. Confocal imaging of the cardiomyocytes demonstrated symmetrical alignment in the same direction on the aligned nanofiber patch in sharp contrast to the random appearance of cardiomyocytes cultured on a tissue culture plate. The hiPSC-CMs cultured on aligned nanofiber cardiac patches showed more efficient calcium cycling compared with cells cultured on standard flat surface culture plates. Quantification of mRNA with qRT-PCR confirmed that these cardiomyocytes expressed α-actinin, troponin-T and connexin-43 in-vitro. Conclusions Overall, our results demonstrated changes in morphology and function of human induced pluripotent derived cardiomyocytes cultured in an anisotropic environment created by an aligned nanofiber patch. In this environment, these cells better approximate normal cardiac tissue compared with cells cultured on flat surface and can serve as the basis for bioengineering of an implantable cardiac patch. PMID:25993466

Evaluation of Changes in Morphology and Function of Human Induced Pluripotent Stem Cell Derived Cardiomyocytes (HiPSC-CMs) Cultured on an Aligned-Nanofiber Cardiac Patch.

PubMed

Khan, Mahmood; Xu, Yanyi; Hua, Serena; Johnson, Jed; Belevych, Andriy; Janssen, Paul M L; Gyorke, Sandor; Guan, Jianjun; Angelos, Mark G

2015-01-01

Dilated cardiomyopathy is a major cause of progressive heart failure. Utilization of stem cell therapy offers a potential means of regenerating viable cardiac tissue. However, a major obstacle to stem cell therapy is the delivery and survival of implanted stem cells in the ischemic heart. To address this issue, we have developed a biomimetic aligned nanofibrous cardiac patch and characterized the alignment and function of human inducible pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) cultured on this cardiac patch. This hiPSC-CMs seeded patch was compared with hiPSC-CMs cultured on standard flat cell culture plates. hiPSC-CMs were cultured on; 1) a highly aligned polylactide-co-glycolide (PLGA) nanofiber scaffold (~50 microns thick) and 2) on a standard flat culture plate. Scanning electron microscopy (SEM) was used to determine alignment of PLGA nanofibers and orientation of the cells on the respective surfaces. Analysis of gap junctions (Connexin-43) was performed by confocal imaging in both the groups. Calcium cycling and patch-clamp technique were performed to measure calcium transients and electrical coupling properties of cardiomyocytes. SEM demonstrated >90% alignment of the nanofibers in the patch which is similar to the extracellular matrix of decellularized rat myocardium. Confocal imaging of the cardiomyocytes demonstrated symmetrical alignment in the same direction on the aligned nanofiber patch in sharp contrast to the random appearance of cardiomyocytes cultured on a tissue culture plate. The hiPSC-CMs cultured on aligned nanofiber cardiac patches showed more efficient calcium cycling compared with cells cultured on standard flat surface culture plates. Quantification of mRNA with qRT-PCR confirmed that these cardiomyocytes expressed α-actinin, troponin-T and connexin-43 in-vitro. Overall, our results demonstrated changes in morphology and function of human induced pluripotent derived cardiomyocytes cultured in an anisotropic environment created by an aligned nanofiber patch. In this environment, these cells better approximate normal cardiac tissue compared with cells cultured on flat surface and can serve as the basis for bioengineering of an implantable cardiac patch.

Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment

PubMed Central

2013-01-01

Background Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Currently, most analysis, especially the identification of conserved regions, relies heavily on Multiple Sequence Alignment and its various heuristics such as progressive alignment, whose run time grows with the square of the number and the length of the aligned sequences and requires significant computational resources. In this work, we present a method to efficiently discover regions of high similarity across multiple sequences without performing expensive sequence alignment. The method is based on approximating edit distance between segments of sequences using p-mer frequency counts. Then, efficient high-throughput data stream clustering is used to group highly similar segments into so called quasi-alignments. Quasi-alignments have numerous applications such as identifying species and their taxonomic class from sequences, comparing sequences for similarities, and, as in this paper, discovering conserved regions across related sequences. Results In this paper, we show that quasi-alignments can be used to discover highly similar segments across multiple sequences from related or different genomes efficiently and accurately. Experiments on a large number of unaligned 16S rRNA sequences obtained from the Greengenes database show that the method is able to identify conserved regions which agree with known hypervariable regions in 16S rRNA. Furthermore, the experiments show that the proposed method scales well for large data sets with a run time that grows only linearly with the number and length of sequences, whereas for existing multiple sequence alignment heuristics the run time grows super-linearly. Conclusion Quasi-alignment-based algorithms can detect highly similar regions and conserved areas across multiple sequences. Since the run time is linear and the sequences are converted into a compact clustering model, we are able to identify conserved regions fast or even interactively using a standard PC. Our method has many potential applications such as finding characteristic signature sequences for families of organisms and studying conserved and variable regions in, for example, 16S rRNA. PMID:24564200

Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment.

PubMed

Nagar, Anurag; Hahsler, Michael

2013-01-01

Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Currently, most analysis, especially the identification of conserved regions, relies heavily on Multiple Sequence Alignment and its various heuristics such as progressive alignment, whose run time grows with the square of the number and the length of the aligned sequences and requires significant computational resources. In this work, we present a method to efficiently discover regions of high similarity across multiple sequences without performing expensive sequence alignment. The method is based on approximating edit distance between segments of sequences using p-mer frequency counts. Then, efficient high-throughput data stream clustering is used to group highly similar segments into so called quasi-alignments. Quasi-alignments have numerous applications such as identifying species and their taxonomic class from sequences, comparing sequences for similarities, and, as in this paper, discovering conserved regions across related sequences. In this paper, we show that quasi-alignments can be used to discover highly similar segments across multiple sequences from related or different genomes efficiently and accurately. Experiments on a large number of unaligned 16S rRNA sequences obtained from the Greengenes database show that the method is able to identify conserved regions which agree with known hypervariable regions in 16S rRNA. Furthermore, the experiments show that the proposed method scales well for large data sets with a run time that grows only linearly with the number and length of sequences, whereas for existing multiple sequence alignment heuristics the run time grows super-linearly. Quasi-alignment-based algorithms can detect highly similar regions and conserved areas across multiple sequences. Since the run time is linear and the sequences are converted into a compact clustering model, we are able to identify conserved regions fast or even interactively using a standard PC. Our method has many potential applications such as finding characteristic signature sequences for families of organisms and studying conserved and variable regions in, for example, 16S rRNA.

Chiropractic in North America: toward a strategic plan for professional renewal--outcomes from the 2006 Chiropractic Strategic Planning Conference.

PubMed

Triano, John J; Goertz, Christine; Weeks, John; Murphy, Donald R; Kranz, Karl C; McClelland, George C; Kopansky-Giles, Deborah; Morgan, William; Nelson, Craig F

2010-06-01

This report describes the process, participation, and recommendations of a set of consensus conferences on strategy for professional growth that emphasized elements of public trust and alignment between the chiropractic profession and its stakeholders. In February and August 2006, an invitational group of leaders in the chiropractic profession convened an ad hoc Chiropractic Strategic Planning Conference. Public notice was given and support solicited through the Foundation of Chiropractic Education and Research. A series of international and interdisciplinary speakers gave presentations on the shifting of external social dynamics and medical culture, illuminating opportunities for the profession to extend its privilege and service. A systematic round-robin discussion was followed by group breakout sessions to develop recommendations on priorities for the profession to respond to challenges and opportunities. Recommendations were reviewed by the group as a whole and voted to consensus requiring more than 70% agreement. Participants determined a series of recommendations within 5 key domains for improving health professions practice: education, research, regulation, workplace, and leadership. The action steps proposed by the Strategic Planning Committee are first steps to provide better service to the public while making use of the inherent strengths of the profession. Copyright (c) 2010 National University of Health Sciences. Published by Mosby, Inc. All rights reserved.

Molecular detection of Sarcocystis lutrae in the European badger (Meles meles) in Scotland.

PubMed

Lepore, T; Bartley, P M; Chianini, F; Macrae, A I; Innes, E A; Katzer, F

2017-09-01

Neck samples from 54 badgers and 32 tongue samples of the same badgers (Meles meles), collected in the Lothians and Borders regions of Scotland, were tested using polymerase chain reactions (PCRs) directed against the 18S ribosomal DNA and the internal transcribed spacer (ITS1) region of protozoan parasites of the family Sarcocystidae. Positive results were obtained from 36/54 (67%) neck and 24/32 (75%) tongue samples using an 18S rDNA PCR. A 468 base pair consensus sequence that was generated from the 18S rDNA PCR amplicons (KX229728) showed 100% identity to Sarcocystis lutrae. The ITS1 PCR results revealed that 12/20 (60%) neck and 10/20 (50%) tongue samples were positive for Sarcocystidae DNA. A 1074 bp consensus sequence was generated from the ITS1 PCR amplicons (KX431307) and showed 100% identity to S. lutrae. Multiple sequence alignments and phylogenetic analysis support the finding that the rDNA found in badgers is identical to that of S. lutrae. This parasite has not been previously reported in badgers or in the UK. Sarcocystis lutrae has previously only been detected in tongue, skeletal muscle and diaphragm samples of the Eurasian otter (Lutra lutra) in Norway and potentially in the Arctic fox (Vulpes lagopus).

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides

PubMed Central

Tsirigos, Konstantinos D.; Peters, Christoph; Shu, Nanjiang; Käll, Lukas; Elofsson, Arne

2015-01-01

TOPCONS (http://topcons.net/) is a widely used web server for consensus prediction of membrane protein topology. We hereby present a major update to the server, with some substantial improvements, including the following: (i) TOPCONS can now efficiently separate signal peptides from transmembrane regions. (ii) The server can now differentiate more successfully between globular and membrane proteins. (iii) The server now is even slightly faster, although a much larger database is used to generate the multiple sequence alignments. For most proteins, the final prediction is produced in a matter of seconds. (iv) The user-friendly interface is retained, with the additional feature of submitting batch files and accessing the server programmatically using standard interfaces, making it thus ideal for proteome-wide analyses. Indicatively, the user can now scan the entire human proteome in a few days. (v) For proteins with homology to a known 3D structure, the homology-inferred topology is also displayed. (vi) Finally, the combination of methods currently implemented achieves an overall increase in performance by 4% as compared to the currently available best-scoring methods and TOPCONS is the only method that can identify signal peptides and still maintain a state-of-the-art performance in topology predictions. PMID:25969446

Eigenbeam analysis of the diversity in bat biosonar beampatterns.

PubMed

Caspers, Philip; Müller, Rolf

2015-03-01

A quantitative analysis of the interspecific variability in bat biosonar beampatterns has been carried out on 267 numerical predictions of emission and reception beampatterns from 98 different species. Since these beampatterns did not share a common orientation, an alignment was necessary to analyze the variability in the shape of the patterns. To achieve this, beampatterns were aligned using a pairwise optimization framework based on a rotation-dependent cost function. The sum of the p-norms between beam-gain functions across frequency served as a figure of merit. For a representative subset of the data, it was found that all pairwise beampattern alignments resulted in a unique global minimum. This minimum was found to be contained in a subset of all possible beampattern rotations that could be predicted by the overall beam orientation. Following alignment, the beampatterns were decomposed into principal components. The average beampattern consisted of a symmetric, positionally static single lobe that narrows and became progressively asymmetric with increasing frequency. The first three "eigenbeams" controlled the beam width of the beampattern across frequency while higher rank eigenbeams account for symmetry and lobe motion. Reception and emission beampatterns could be distinguished (85% correct classification) based on the first 14 eigenbeams.

Diameter and Geometry Control of Vertically Aligned SWNTs through Catalyst Manipulation

NASA Astrophysics Data System (ADS)

Xiang, Rong; Einarsson, Erik; Okawa, Jun; Murakami, Yoichi; Maruyama, Shigeo

2009-03-01

We present our recent progress on manipulating our liquid-based catalyst loading process, which possesses greater potential than conventional deposition in terms of cost and scalability, to control the diameter and morphology of single-walled carbon nanotubes (SWNTs). We demonstrate that the diameter of aligned SWNTs synthesized by alcohol catalytic CVD can be tailored over a wide range by modifying the catalyst recipe. SWNT arrays with an average diameter as small as 1.2 nm were obtained by this method. Additionally, owing to the alignment of the array, the continuous change of the SWNT diameter during a single CVD process can be clearly observed and quantitatively characterized. We have also developed a versatile wet chemistry method to localize the growth of SWNTs to desired regions via surface modification. By functionalizing the silicon surface using a classic self-assembled monolayer, the catalyst can be selectively dip-coated onto hydrophilic areas of the substrate. This technique was successful in producing both random and aligned SWNTs with various patterns. The precise control of the diameter and morphology of SWNTs, achieved by simple and scalable liquid-based surface chemistry, could greatly facilitate the application of SWNTs as the building blocks of future nano-devices.

Kinematic alignment technique for total hip and knee arthroplasty

PubMed Central

Rivière, Charles; Lazic, Stefan; Villet, Loïc; Wiart, Yann; Allwood, Sarah Muirhead; Cobb, Justin

2018-01-01

Conventional techniques for hip and knee arthroplasty have led to good long-term clinical outcomes, but complications remain despite better surgical precision and improvements in implant design and quality. Technological improvements and a better understanding of joint kinematics have facilitated the progression to ‘personalized’ implant positioning (kinematic alignment) for total hip (THA) and knee (TKA) arthroplasty, the true value of which remains to be determined. By achieving a true knee resurfacing, the kinematic alignment (KA) technique for TKA aims at aligning the components with the physiological kinematic axes of the knee and restoring the constitutional tibio-femoral joint line frontal and axial orientation and soft-tissue laxity. The KA technique for THA aims at restoring the native ‘combined femoro-acetabular anteversion’ and the hip’s centre of rotation, and occasionally adjusting the cup position and design based on the assessment of the individual spine-hip relation. The key element for optimal prosthetic joint kinematics (hip or knee) is to reproduce the femoral anatomy. The transverse acetabular ligament (TAL) is the reference landmark to adjust the cup position. Cite this article: EFORT Open Rev 2018;3:98-105. DOI: 10.1302/2058-5241.3.170022 PMID:29657851

StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase

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

Zemla, A; Lang, D; Kostova, T

2010-11-29

Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more satisfactory - still, they cannot provide reliable results at low levels of sequence identity. Our goal in the current work was to develop an algorithm that could overcome these difficulties and facilitatemore » the identification of structurally (and possibly functionally) relevant residue-residue correspondences between compared protein structures. Here we present StralSV, a new algorithm for detecting closely related structure fragments and quantifying residue frequency from tight local structure alignments. We apply StralSV in a study of the RNA-dependent RNA polymerase of poliovirus and demonstrate that the algorithm can be used to determine regions of the protein that are relatively unique or that shared structural similarity with structures that are distantly related. By quantifying residue frequencies among many residue-residue pairs extracted from local alignments, one can infer potential structural or functional importance of specific residues that are determined to be highly conserved or that deviate from a consensus. We further demonstrate that considerable detailed structural and phylogenetic information can be derived from StralSV analyses. StralSV is a new structure-based algorithm for identifying and aligning structure fragments that have similarity to a reference protein. StralSV analysis can be used to quantify residue-residue correspondences and identify residues that may be of particular structural or functional importance, as well as unusual or unexpected residues at a given sequence position.« less

Different phylogenomic approaches to resolve the evolutionary relationships among model fish species.

PubMed

Negrisolo, Enrico; Kuhl, Heiner; Forcato, Claudio; Vitulo, Nicola; Reinhardt, Richard; Patarnello, Tomaso; Bargelloni, Luca

2010-12-01

Comparative genomics holds the promise to magnify the information obtained from individual genome sequencing projects, revealing common features conserved across genomes and identifying lineage-specific characteristics. To implement such a comparative approach, a robust phylogenetic framework is required to accurately reconstruct evolution at the genome level. Among vertebrate taxa, teleosts represent the second best characterized group, with high-quality draft genome sequences for five model species (Danio rerio, Gasterosteus aculeatus, Oryzias latipes, Takifugu rubripes, and Tetraodon nigroviridis), and several others are in the finishing lane. However, the relationships among the acanthomorph teleost model fishes remain an unresolved taxonomic issue. Here, a genomic region spanning over 1.2 million base pairs was sequenced in the teleost fish Dicentrarchus labrax. Together with genomic data available for the above fish models, the new sequence was used to identify unique orthologous genomic regions shared across all target taxa. Different strategies were applied to produce robust multiple gene and genomic alignments spanning from 11,802 to 186,474 amino acid/nucleotide positions. Ten data sets were analyzed according to Bayesian inference, maximum likelihood, maximum parsimony, and neighbor joining methods. Extensive analyses were performed to explore the influence of several factors (e.g., alignment methodology, substitution model, data set partitions, and long-branch attraction) on the tree topology. Although a general consensus was observed for a closer relationship between G. aculeatus (Gasterosteidae) and Di. labrax (Moronidae) with the atherinomorph O. latipes (Beloniformes) sister taxon of this clade, with the tetraodontiform group Ta. rubripes and Te. nigroviridis (Tetraodontiformes) representing a more distantly related taxon among acanthomorph model fish species, conflicting results were obtained between data sets and methods, especially with respect to the choice of alignment methodology applied to noncoding parts of the genomic region under study. This may limit the use of intergenic/noncoding sequences in phylogenomics until more robust alignment algorithms are developed.

Large Volume, Optical and Opto-Mechanical Metrology Techniques for ISIM on JWST

NASA Technical Reports Server (NTRS)

Hadjimichael, Theo

2015-01-01

The final, flight build of the Integrated Science Instrument Module (ISIM) element of the James Webb Space Telescope is the culmination of years of work across many disciplines and partners. This paper covers the large volume, ambient, optical and opto-mechanical metrology techniques used to verify the mechanical integration of the flight instruments in ISIM, including optical pupil alignment. We present an overview of ISIM's integration and test program, which is in progress, with an emphasis on alignment and optical performance verification. This work is performed at NASA Goddard Space Flight Center, in close collaboration with the European Space Agency, the Canadian Space Agency, and the Mid-Infrared Instrument European Consortium.

The wisdom of the commons: ensemble tree classifiers for prostate cancer prognosis.

PubMed

Koziol, James A; Feng, Anne C; Jia, Zhenyu; Wang, Yipeng; Goodison, Seven; McClelland, Michael; Mercola, Dan

2009-01-01

Classification and regression trees have long been used for cancer diagnosis and prognosis. Nevertheless, instability and variable selection bias, as well as overfitting, are well-known problems of tree-based methods. In this article, we investigate whether ensemble tree classifiers can ameliorate these difficulties, using data from two recent studies of radical prostatectomy in prostate cancer. Using time to progression following prostatectomy as the relevant clinical endpoint, we found that ensemble tree classifiers robustly and reproducibly identified three subgroups of patients in the two clinical datasets: non-progressors, early progressors and late progressors. Moreover, the consensus classifications were independent predictors of time to progression compared to known clinical prognostic factors.

Bovine xenograft application for treatment of a metatarsal nonunion fracture in an alpaca (Vicugna pacos).

PubMed

Longo, F; Finotti, L; Bellini, L; Zavan, B; Busetto, R; Isola, M

2016-05-01

A 15-year-old female huacaya alpaca (Vicugna pacos) was referred because of a non-weight-bearing lameness (4/4) in the left pelvic limb caused by a grade three open metatarsal fracture. The referring veterinarian treated the fracture with conservative management using bandages, but it progressively evolved to a non-union. Clinical examination revealed external wounds on the medial and lateral surfaces of the metatarsus. Radiographs confirmed an open, nonarticular, displaced, diaphyseal fracture of the left metatarsus. Cancellous bone was sourced from bovine proximal and distal femur epiphyses, followed by a thermal shock procedure to achieve decellularisation, to produce a xenograft. Open reduction and internal fixation of the fracture using locking plates was performed. Alignment of the fracture fragments was corrected and the xenograft was placed at the debrided fracture site to stimulate and harness osteogenesis in situ. Clinical and radiographic follow-up was performed up to 40 weeks postoperatively. Clinical evaluations revealed that the alpaca gradually increased weight bearing following bandage removal 10 days after surgery. Serial radiographs showed correct alignment of the left metatarsus, progressive bone modelling and, complete bone union at 12 weeks. Ten months postoperatively the alpaca showed no signs of lameness and resumed normal activity. For management of a metatarsal non-union, a combination of bovine xenograft application and angular stable internal fixation progressed toward an excellent long-term recovery.

Enhanced antibacterial activity through the controlled alignment of graphene oxide nanosheets.

PubMed

Lu, Xinglin; Feng, Xunda; Werber, Jay R; Chu, Chiheng; Zucker, Ines; Kim, Jae-Hong; Osuji, Chinedum O; Elimelech, Menachem

2017-11-14

The cytotoxicity of 2D graphene-based nanomaterials (GBNs) is highly important for engineered applications and environmental health. However, the isotropic orientation of GBNs, most notably graphene oxide (GO), in previous experimental studies obscured the interpretation of cytotoxic contributions of nanosheet edges. Here, we investigate the orientation-dependent interaction of GBNs with bacteria using GO composite films. To produce the films, GO nanosheets are aligned in a magnetic field, immobilized by cross-linking of the surrounding matrix, and exposed on the surface through oxidative etching. Characterization by small-angle X-ray scattering and atomic force microscopy confirms that GO nanosheets align progressively well with increasing magnetic field strength and that the alignment is effectively preserved by cross-linking. When contacted with the model bacterium Escherichia coli , GO nanosheets with vertical orientation exhibit enhanced antibacterial activity compared with random and horizontal orientations. Further characterization is performed to explain the enhanced antibacterial activity of the film with vertically aligned GO. Using phospholipid vesicles as a model system, we observe that GO nanosheets induce physical disruption of the lipid bilayer. Additionally, we find substantial GO-induced oxidation of glutathione, a model intracellular antioxidant, paired with limited generation of reactive oxygen species, suggesting that oxidation occurs through a direct electron-transfer mechanism. These physical and chemical mechanisms both require nanosheet penetration of the cell membrane, suggesting that the enhanced antibacterial activity of the film with vertically aligned GO stems from an increased density of edges with a preferential orientation for membrane disruption. The importance of nanosheet penetration for cytotoxicity has direct implications for the design of engineering surfaces using GBNs.

How much is too much assessment? Insight into assessment-driven student learning gains in large-scale undergraduate microbiology courses.

PubMed

Wang, Jack T H; Schembri, Mark A; Hall, Roy A

2013-01-01

Designing and implementing assessment tasks in large-scale undergraduate science courses is a labor-intensive process subject to increasing scrutiny from students and quality assurance authorities alike. Recent pedagogical research has provided conceptual frameworks for teaching introductory undergraduate microbiology, but has yet to define best-practice assessment guidelines. This study assessed the applicability of Biggs' theory of constructive alignment in designing consistent learning objectives, activities, and assessment items that aligned with the American Society for Microbiology's concept-based microbiology curriculum in MICR2000, an introductory microbiology course offered at the University of Queensland, Australia. By improving the internal consistency in assessment criteria and increasing the number of assessment items explicitly aligned to the course learning objectives, the teaching team was able to efficiently provide adequate feedback on numerous assessment tasks throughout the semester, which contributed to improved student performance and learning gains. When comparing the constructively aligned 2011 offering of MICR2000 with its 2010 counterpart, students obtained higher marks in both coursework assignments and examinations as the semester progressed. Students also valued the additional feedback provided, as student rankings for course feedback provision increased in 2011 and assessment and feedback was identified as a key strength of MICR2000. By designing MICR2000 using constructive alignment and iterative assessment tasks that followed a common set of learning outcomes, the teaching team was able to effectively deliver detailed and timely feedback in a large introductory microbiology course. This study serves as a case study for how constructive alignment can be integrated into modern teaching practices for large-scale courses.

SPHERE: SPherical Harmonic Elastic REgistration of HARDI Data

PubMed Central

Yap, Pew-Thian; Chen, Yasheng; An, Hongyu; Yang, Yang; Gilmore, John H.; Lin, Weili

2010-01-01

In contrast to the more common Diffusion Tensor Imaging (DTI), High Angular Resolution Diffusion Imaging (HARDI) allows superior delineation of angular microstructures of brain white matter, and makes possible multiple-fiber modeling of each voxel for better characterization of brain connectivity. However, the complex orientation information afforded by HARDI makes registration of HARDI images more complicated than scalar images. In particular, the question of how much orientation information is needed for satisfactory alignment has not been sufficiently addressed. Low order orientation representation is generally more robust than high order representation, although the latter provides more information for correct alignment of fiber pathways. However, high order representation, when naïvely utilized, might not necessarily be conducive to improving registration accuracy since similar structures with significant orientation differences prior to proper alignment might be mistakenly taken as non-matching structures. We present in this paper a HARDI registration algorithm, called SPherical Harmonic Elastic REgistration (SPHERE), which in a principled means hierarchically extracts orientation information from HARDI data for structural alignment. The image volumes are first registered using robust, relatively direction invariant features derived from the Orientation Distribution Function (ODF), and the alignment is then further refined using spherical harmonic (SH) representation with gradually increasing orders. This progression from non-directional, single-directional to multi-directional representation provides a systematic means of extracting directional information given by diffusion-weighted imaging. Coupled with a template-subject-consistent soft-correspondence-matching scheme, this approach allows robust and accurate alignment of HARDI data. Experimental results show marked increase in accuracy over a state-of-the-art DTI registration algorithm. PMID:21147231

DNA motif alignment by evolving a population of Markov chains.

PubMed

Bi, Chengpeng

2009-01-30

Deciphering cis-regulatory elements or de novo motif-finding in genomes still remains elusive although much algorithmic effort has been expended. The Markov chain Monte Carlo (MCMC) method such as Gibbs motif samplers has been widely employed to solve the de novo motif-finding problem through sequence local alignment. Nonetheless, the MCMC-based motif samplers still suffer from local maxima like EM. Therefore, as a prerequisite for finding good local alignments, these motif algorithms are often independently run a multitude of times, but without information exchange between different chains. Hence it would be worth a new algorithm design enabling such information exchange. This paper presents a novel motif-finding algorithm by evolving a population of Markov chains with information exchange (PMC), each of which is initialized as a random alignment and run by the Metropolis-Hastings sampler (MHS). It is progressively updated through a series of local alignments stochastically sampled. Explicitly, the PMC motif algorithm performs stochastic sampling as specified by a population-based proposal distribution rather than individual ones, and adaptively evolves the population as a whole towards a global maximum. The alignment information exchange is accomplished by taking advantage of the pooled motif site distributions. A distinct method for running multiple independent Markov chains (IMC) without information exchange, or dubbed as the IMC motif algorithm, is also devised to compare with its PMC counterpart. Experimental studies demonstrate that the performance could be improved if pooled information were used to run a population of motif samplers. The new PMC algorithm was able to improve the convergence and outperformed other popular algorithms tested using simulated and biological motif sequences.

Cancer-associated fibroblasts promote directional cancer cell migration by aligning fibronectin.

PubMed

Erdogan, Begum; Ao, Mingfang; White, Lauren M; Means, Anna L; Brewer, Bryson M; Yang, Lijie; Washington, M Kay; Shi, Chanjuan; Franco, Omar E; Weaver, Alissa M; Hayward, Simon W; Li, Deyu; Webb, Donna J

2017-11-06

Cancer-associated fibroblasts (CAFs) are major components of the carcinoma microenvironment that promote tumor progression. However, the mechanisms by which CAFs regulate cancer cell migration are poorly understood. In this study, we show that fibronectin (Fn) assembled by CAFs mediates CAF-cancer cell association and directional migration. Compared with normal fibroblasts, CAFs produce an Fn-rich extracellular matrix with anisotropic fiber orientation, which guides the cancer cells to migrate directionally. CAFs align the Fn matrix by increasing nonmuscle myosin II- and platelet-derived growth factor receptor α-mediated contractility and traction forces, which are transduced to Fn through α5β1 integrin. We further show that prostate cancer cells use αv integrin to migrate efficiently and directionally on CAF-derived matrices. We demonstrate that aligned Fn is a prominent feature of invasion sites in human prostatic and pancreatic carcinoma samples. Collectively, we present a new mechanism by which CAFs organize the Fn matrix and promote directional cancer cell migration. © 2017 Erdogan et al.

Cancer-associated fibroblasts promote directional cancer cell migration by aligning fibronectin

PubMed Central

Ao, Mingfang; White, Lauren M.; Means, Anna L.; Yang, Lijie; Washington, M. Kay; Franco, Omar E.; Li, Deyu; Webb, Donna J.

2017-01-01

Cancer-associated fibroblasts (CAFs) are major components of the carcinoma microenvironment that promote tumor progression. However, the mechanisms by which CAFs regulate cancer cell migration are poorly understood. In this study, we show that fibronectin (Fn) assembled by CAFs mediates CAF–cancer cell association and directional migration. Compared with normal fibroblasts, CAFs produce an Fn-rich extracellular matrix with anisotropic fiber orientation, which guides the cancer cells to migrate directionally. CAFs align the Fn matrix by increasing nonmuscle myosin II- and platelet-derived growth factor receptor α–mediated contractility and traction forces, which are transduced to Fn through α5β1 integrin. We further show that prostate cancer cells use αv integrin to migrate efficiently and directionally on CAF-derived matrices. We demonstrate that aligned Fn is a prominent feature of invasion sites in human prostatic and pancreatic carcinoma samples. Collectively, we present a new mechanism by which CAFs organize the Fn matrix and promote directional cancer cell migration. PMID:29021221

Microwave purification of large-area horizontally aligned arrays of single-walled carbon nanotubes.

PubMed

Xie, Xu; Jin, Sung Hun; Wahab, Muhammad A; Islam, Ahmad E; Zhang, Chenxi; Du, Frank; Seabron, Eric; Lu, Tianjian; Dunham, Simon N; Cheong, Hou In; Tu, Yen-Chu; Guo, Zhilin; Chung, Ha Uk; Li, Yuhang; Liu, Yuhao; Lee, Jong-Ho; Song, Jizhou; Huang, Yonggang; Alam, Muhammad A; Wilson, William L; Rogers, John A

2014-11-12

Recent progress in the field of single-walled carbon nanotubes (SWNTs) significantly enhances the potential for practical use of this remarkable class of material in advanced electronic and sensor devices. One of the most daunting challenges is in creating large-area, perfectly aligned arrays of purely semiconducting SWNTs (s-SWNTs). Here we introduce a simple, scalable, large-area scheme that achieves this goal through microwave irradiation of aligned SWNTs grown on quartz substrates. Microstrip dipole antennas of low work-function metals concentrate the microwaves and selectively couple them into only the metallic SWNTs (m-SWNTs). The result allows for complete removal of all m-SWNTs, as revealed through systematic experimental and computational studies of the process. As one demonstration of the effectiveness, implementing this method on large arrays consisting of ~20,000 SWNTs completely removes all of the m-SWNTs (~7,000) to yield a purity of s-SWNTs that corresponds, quantitatively, to at least to 99.9925% and likely significantly higher.

Diagnosis and management of non-alcoholic fatty liver disease and related metabolic disorders: consensus statement from the Study Group of Liver and Metabolism, Chinese Society of Endocrinology.

PubMed

Gao, Xin; Fan, Jian-Gao

2013-12-01

Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease in Western countries, affecting 20%-33% of the general population. Large population-based surveys in China indicate a prevalence of approximately 15%-30%. Worldwide, including in China, the prevalence of NAFLD has increased rapidly in parallel with regional trends of obesity, type 2 diabetes and metabolic syndrome. In addition, NAFLD has contributed significantly to increased overall, as well as cardiovascular and liver-related, mortality in the general population. In view of rapid advances in research into NAFLD in recent years, this consensus statement provides a brief update on the progress in the field and suggests preferred approaches for the comprehensive management of NAFLD and its related metabolic diseases. © 2013 Ruijin Hospital, Shanghai Jiaotong University School of Medicine and Wiley Publishing Asia Pty Ltd.

Progress toward Consensus Estimates of Regional Glacier Mass Balances for IPCC AR5

NASA Astrophysics Data System (ADS)

Arendt, A. A.; Gardner, A. S.; Cogley, J. G.

2011-12-01

Glaciers are potentially large contributors to rising sea level. Since the last IPCC report in 2007 (AR4), there has been a widespread increase in the use of geodetic observations from satellite and airborne platforms to complement field observations of glacier mass balance, as well as significant improvements in the global glacier inventory. Here we summarize our ongoing efforts to integrate data from multiple sources to arrive at a consensus estimate for each region, and to quantify uncertainties in those estimates. We will use examples from Alaska to illustrate methods for combining Gravity Recovery and Climate Experiment (GRACE), elevation differencing and field observations into a single time series with related uncertainty estimates. We will pay particular attention to reconciling discrepancies between GRACE estimates from multiple processing centers. We will also investigate the extent to which improvements in the glacier inventory affect the accuracy of our regional mass balances.

The future of surgical training in the context of the 'Shape of Training' Review: Consensus recommendations by the Association of Surgeons in Training.

PubMed

Harries, Rhiannon L; Williams, Adam P; Ferguson, Henry J M; Mohan, Helen M; Beamish, Andrew J; Gokani, Vimal J

2016-11-01

ASiT has long maintained that in order to provide the best quality care to patients in the UK and Republic of Ireland, it is critical that surgeons are trained to the highest standards. In addition, it is imperative that surgery remains an attractive career choice, with opportunities for career progression and job satisfaction to attract and retain the best candidates. In 2013, the Shape of Training review report set out recommendations for the structure and delivery of postgraduate training in light of an ever increasingly poly-morbid and ageing population. This consensus statement outlines ASIT's position regarding recommendations for improving surgical training and aims to help guide discussions with regard to future proposed changes to surgical training. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Defining Outcome Measures for Psoriasis: The IDEOM Report from the GRAPPA 2016 Annual Meeting.

PubMed

Callis Duffin, Kristina; Gottlieb, Alice B; Merola, Joseph F; Latella, John; Garg, Amit; Armstrong, April W

2017-05-01

The International Dermatology Outcome Measures (IDEOM) psoriasis working group was established to develop core domains and measurements sets for psoriasis clinical trials and ultimately clinical practice. At the 2016 annual meeting of the Group for Research and Assessment of Psoriasis and Psoriatic Arthritis, the IDEOM psoriasis group presented an overview of its progress toward developing this psoriasis core domain set. First, it summarized the February 2016 meeting of all involved with the IDEOM, highlighting patient and payer perspectives on outcome measures. Second, the group presented an overview of the consensus process for developing the core domain set for psoriasis, including previous literature reviews, nominal group exercises, and meeting discussions. Future plans include the development of working groups to review candidate measures for at least 2 of the domains, including primary pathophysiologic manifestations and patient-reported outcomes, and Delphi surveys to gain consensus on the final psoriasis core domain set.

Laboratory for Computer Science Progress Report 21, July 1983-June 1984.

DTIC Science & Technology

1984-06-01

Systems 269 4. Distributed Consensus 270 5. Election of a Leader in a Distributed Ring of Processors 273 6. Distributed Network Algorithms 274 7. Diagnosis...multiprocessor systems. This facility, funded by the new!y formed Strategic Computing Program of the Defense Advanced Research Projects Agency, will enable...Academic Staff P. Szo)ovits, Group Leader R. Patil Collaborating Investigators M. Criscitiello, M.D., Tufts-New England Medical Center Hospital R

U.S. History Framework for the 1994 National Assessment of Educational Progress. NAEP U.S. History Consensus Project.

ERIC Educational Resources Information Center

Selden, Ramsay; Ward, Thomas G.

The 1994 U.S. History Framework encourages students to learn about ideas and people and to understand how the present world is the result of choices and convictions of people, and the focus of the assessment is to see what diverse U.S. students in grades 4, 8, and 12 understand about U.S. history. The framework proposes that students studying U.S.…

Distant view of the ISS as OV-104 makes its initial approach during STS-106

NASA Image and Video Library

2000-09-09

S106-E-5057 (10 September 2000) --- The International Space Station (ISS) is only a few hundred meters away from the Space Shuttle Atlantis in this electronic image. The last time astronauts saw the ISS, it was not sporting the recently-arriving Progress, which appears at the top in this perspective. Also, next to the Progress, appears the Zvezda service module, which had been delivered by a Proton rocket since the most recent human visit to ISS. The ruled markings in the upper right are part of the Crew Optical Alignment Sight (COAS) on Atlantis.

Creationism and intelligent design are incompatible with scientific progress: A response to Shanta and Vêdanta

PubMed Central

Caetano-Anollés, Gustavo

2016-01-01

ABSTRACT In a recent opinion paper, B.K. Shanta claims science leaves no room for the subjective aspect of consciousness, and in doing so, attacks both origin of life and evolutionary research. He claims Vêdanta, one of the 6 orthodox schools of Hindu philosophy, offers an explanation: “the origin of everything material and nonmaterial is sentient and absolute.” Here I discuss how the pseudoscience of these creationist views, which are aligned with Intelligent Design, are incompatible with scientific progress and should not be published in scientific journals. PMID:27066185

Large-scale Health Information Database and Privacy Protection.

PubMed

Yamamoto, Ryuichi

2016-09-01

Japan was once progressive in the digitalization of healthcare fields but unfortunately has fallen behind in terms of the secondary use of data for public interest. There has recently been a trend to establish large-scale health databases in the nation, and a conflict between data use for public interest and privacy protection has surfaced as this trend has progressed. Databases for health insurance claims or for specific health checkups and guidance services were created according to the law that aims to ensure healthcare for the elderly; however, there is no mention in the act about using these databases for public interest in general. Thus, an initiative for such use must proceed carefully and attentively. The PMDA projects that collect a large amount of medical record information from large hospitals and the health database development project that the Ministry of Health, Labour and Welfare (MHLW) is working on will soon begin to operate according to a general consensus; however, the validity of this consensus can be questioned if issues of anonymity arise. The likelihood that researchers conducting a study for public interest would intentionally invade the privacy of their subjects is slim. However, patients could develop a sense of distrust about their data being used since legal requirements are ambiguous. Nevertheless, without using patients' medical records for public interest, progress in medicine will grind to a halt. Proper legislation that is clear for both researchers and patients will therefore be highly desirable. A revision of the Act on the Protection of Personal Information is currently in progress. In reality, however, privacy is not something that laws alone can protect; it will also require guidelines and self-discipline. We now live in an information capitalization age. I will introduce the trends in legal reform regarding healthcare information and discuss some basics to help people properly face the issue of health big data and privacy protection with a sense of ownership.

Large-scale Health Information Database and Privacy Protection*1

PubMed Central

YAMAMOTO, Ryuichi

2016-01-01

Japan was once progressive in the digitalization of healthcare fields but unfortunately has fallen behind in terms of the secondary use of data for public interest. There has recently been a trend to establish large-scale health databases in the nation, and a conflict between data use for public interest and privacy protection has surfaced as this trend has progressed. Databases for health insurance claims or for specific health checkups and guidance services were created according to the law that aims to ensure healthcare for the elderly; however, there is no mention in the act about using these databases for public interest in general. Thus, an initiative for such use must proceed carefully and attentively. The PMDA*2 projects that collect a large amount of medical record information from large hospitals and the health database development project that the Ministry of Health, Labour and Welfare (MHLW) is working on will soon begin to operate according to a general consensus; however, the validity of this consensus can be questioned if issues of anonymity arise. The likelihood that researchers conducting a study for public interest would intentionally invade the privacy of their subjects is slim. However, patients could develop a sense of distrust about their data being used since legal requirements are ambiguous. Nevertheless, without using patients’ medical records for public interest, progress in medicine will grind to a halt. Proper legislation that is clear for both researchers and patients will therefore be highly desirable. A revision of the Act on the Protection of Personal Information is currently in progress. In reality, however, privacy is not something that laws alone can protect; it will also require guidelines and self-discipline. We now live in an information capitalization age. I will introduce the trends in legal reform regarding healthcare information and discuss some basics to help people properly face the issue of health big data and privacy protection with a sense of ownership. PMID:28299244

CE: Original Research: Creating an Evidence-Based Progression for Clinical Advancement Programs.

PubMed

Burke, Kathleen G; Johnson, Tonya; Sites, Christine; Barnsteiner, Jane

2017-05-01

: Background: The Institute of Medicine (IOM) and the Quality and Safety Education for Nurses (QSEN) project have identified six nursing competencies and supported their integration into undergraduate and graduate nursing curricula nationwide. But integration of those competencies into clinical practice has been limited, and evidence for the progression of competency proficiency within clinical advancement programs is scant. Using an evidence-based approach and building on the competencies identified by the IOM and QSEN, a team of experts at an academic health system developed eight competency domains and 186 related knowledge, skills, and attitudes (KSAs) for professional nursing practice. The aim of our study was to validate the eight identified competencies and 186 related KSAs and determine their developmental progression within a clinical advancement program. Using the Delphi technique, nursing leadership validated the newly identified competency domains and KSAs as essential to practice. Clinical experts from 13 Magnet-designated hospitals with clinical advancement programs then participated in Delphi rounds aimed at reaching consensus on the developmental progression of the 186 KSAs through four levels of clinical advancement. Two Delphi rounds resulted in consensus by the expert participants. All eight competency domains were determined to be essential at all four levels of clinical practice. At the novice level of practice, the experts identified a greater number of KSAs in the domains of safety and patient- and family-centered care. At more advanced practice levels, the experts identified a greater number of KSAs in the domains of professionalism, teamwork, technology and informatics, and continuous quality improvement. Incorporating the eight competency domains and the 186 KSAs into a framework for clinical advancement programs will likely result in more clearly defined role expectations; enhance accountability; and elevate and promote nursing practice, thereby improving clinical outcomes and quality of care. With their emphasis on quality and safety, the eight competency domains also offer a framework for enhancing position descriptions, performance evaluations, clinical recognition, initial and ongoing competency assessment programs, and orientation and residency programs.

Chemical Communications

DTIC Science & Technology

2012-10-26

the need for alignment. We have also demonstrated the use of this technique with various materials as masks for silk biopolymer RIE processing and a...project. The automatization of silk solution was developed. Examination of different processing conditions for the raw material showed promise for...higher durability and higher flexibility optical substrates. Progress on interfaces was solidified. The previous findings on silk -metal interfaces

Strategy Precedes Operational Effectiveness: Aligning High Graduation Rankings with Competitive Graduation Grade Point Averages

ERIC Educational Resources Information Center

Apprey, Maurice; Bassett, Kimberley C.; Preston-Grimes, Patrice; Lewis, Dion W.; Wood, Beverly

2014-01-01

Two pivotal and interconnected claims are addressed in this article. First, strategy precedes program effectiveness. Second, graduation rates and rankings are insufficient in any account of academic progress for African American students. In this article, graduation is regarded as the floor and not the ceiling, as it were. The ideal situation in…

The Development of the easyCBM CCSS Reading Assessments: Grade 3. Technical Report #1221

ERIC Educational Resources Information Center

Alonzo, Julie; Park, Bitnara Jasmine; Tindal, Gerald

2012-01-01

In this technical report, we document the development and piloting of easyCBM reading measures aligned to the Common Core State Standards, designed for use in screening students at risk for reading difficulty and monitoring their progress as they develop reading skills. The measures, which assess students' ability to respond to…

Phoneme Segmenting Alignment with the Common Core Foundational Skills Standard Two: Grades K-1. Technical Report #1227

ERIC Educational Resources Information Center

Sáez, Leilani; Irvin, P. Shawn; Alonzo, Julie; Tindal, Gerald

2012-01-01

In 2006, the easyCBM reading assessment system was developed to support the progress monitoring of phoneme segmenting, letter names and sounds recognition, word reading, passage reading fluency, and comprehension skill development in elementary schools. More recently, the Common Core Standards in English Language Arts have been introduced as a…

Assessment Update: Progress, Trends, and Practices in Higher Education. Volume 24, Issue 3, May-June 2012

ERIC Educational Resources Information Center

Banta, Trudy W., Ed.

2012-01-01

This issue of "Assessment Update" presents the following articles: (1) A "Wisdom of Crowds" Approach to Outcomes Assessment (Gregory Burton); (2) Editor's Notes: Collective Assessment and DQP Follow-Up (Trudy W. Banta); (3) Satisfaction with Data Management Systems in Standards-Based Alignment (Brett Everhart and Jeanne M.…

Development of Perceived Instrumentality for Mathematics, Reading and Science Curricula

ERIC Educational Resources Information Center

Garcia, Steve L.

2010-01-01

Perceptions of instrumentality (PI) are the connections one sees between a current activity and a future goal. With high PI, one is motivated to persist with quality effort because the current activity, even when difficult, is perceived as aligned with, and progress toward, the goal. Conversely, with low PI, one is motivated to relinquish effort…

Business Leadership in Global Climate Change Responses

PubMed Central

Esty, Daniel C.

2018-01-01

In the 2015 Paris Climate Change Agreement, 195 countries committed to reducing greenhouse gas emissions in recognition of the scientific consensus on the consequences of climate change, including substantial public health burdens. In June 2017, however, US president Donald Trump announced that the United States would not implement the Paris Agreement. We highlight the business community’s backing for climate change action in the United States. Just as the US federal government is backing away from its Paris commitments, many corporate executives are recognizing the need to address the greenhouse gas emissions of their companies and the business logic of strong environmental, social, and governance practices more generally. We conclude that climate change could emerge as an issue on which the business and public health communities might align and provide leadership. PMID:29698101

[An intriguing model for 5S rDNA sequences dispersion in the genome of freshwater stingray Potamotrygon motoro (Chondrichthyes: Potamotrygonidae)].

PubMed

Cruz, V P; Oliveira, C; Foresti, F

2015-01-01

5S rDNA genes of the stingray Potamotrygon motoro were PCR replicated, purified, cloned and sequenced. Two distinct classes of segments of different sizes were obtained. The smallest, with 342 bp units, was classified as class I, and the largest, with 1900 bp units, was designated as class II. Alignment with the consensus sequences for both classes showed changes in a few bases in the 5S rDNA genes. TATA-like sequences were detected in the nontranscribed spacer (NTS) regions of class I and a microsatellite (GCT) 10 sequence was detected in the NTS region of class II. The results obtained can help to understand the molecular organization of ribosomal genes and the mechanism of gene dispersion.

A Multispectral Image Creating Method for a New Airborne Four-Camera System with Different Bandpass Filters

PubMed Central

Li, Hanlun; Zhang, Aiwu; Hu, Shaoxing

2015-01-01

This paper describes an airborne high resolution four-camera multispectral system which mainly consists of four identical monochrome cameras equipped with four interchangeable bandpass filters. For this multispectral system, an automatic multispectral data composing method was proposed. The homography registration model was chosen, and the scale-invariant feature transform (SIFT) and random sample consensus (RANSAC) were used to generate matching points. For the difficult registration problem between visible band images and near-infrared band images in cases lacking manmade objects, we presented an effective method based on the structural characteristics of the system. Experiments show that our method can acquire high quality multispectral images and the band-to-band alignment error of the composed multiple spectral images is less than 2.5 pixels. PMID:26205264

Business Leadership in Global Climate Change Responses.

PubMed

Esty, Daniel C; Bell, Michelle L

2018-04-01

In the 2015 Paris Climate Change Agreement, 195 countries committed to reducing greenhouse gas emissions in recognition of the scientific consensus on the consequences of climate change, including substantial public health burdens. In June 2017, however, US president Donald Trump announced that the United States would not implement the Paris Agreement. We highlight the business community's backing for climate change action in the United States. Just as the US federal government is backing away from its Paris commitments, many corporate executives are recognizing the need to address the greenhouse gas emissions of their companies and the business logic of strong environmental, social, and governance practices more generally. We conclude that climate change could emerge as an issue on which the business and public health communities might align and provide leadership.

An international Delphi study examining health promotion and health education in nursing practice, education and policy.

PubMed

Whitehead, Dean

2008-04-01

To arrive at an expert consensus in relation to health promotion and health education constructs as they apply to nursing practice, education and policy. Nursing has often been maligned and criticized, both inside and outside of the profession, for its ability to understand and conduct effective health promotion and health education-related activities. In the absence of an expert-based consensus, nurses may find it difficult to progress beyond the current situation. In the absence of any previously published nursing-related consensus research, this study seeks to fill that knowledge-gap. A two-round Delphi technique via email correspondence. A first-round qualitative questionnaire used open-ended questions for defining health promotion and health education. This was both in general terms and as participants believed these concepts related to the clinical, theoretical (academic/educational) and the policy (political) setting in nursing. Line-by-line qualitative content and thematic analysis of the first-round data generated 13 specific categories. These categories contained 134 statement items. The second-round questionnaire comprised the identified 134 statements. Using a five-point Likert scale (ranging from 1 = strongly disagree to 5 = strongly agree) participants scored and rated their level of agreement/disagreement against the listed items. Data from the second-round was descriptively analysed according to distribution and central tendency measures. An expert consensus was reached on 65 of the original 134 statements. While some minor contradiction was demonstrated, strong consensus emerged around the issues of defining health promotion and health education and the emergence of a wider health promotion and health education role for nursing. No consensus was reached on only one of the 13 identified topic categories - that of 'nurses working with other disciplines and agencies in a health education and health promotion role.' This study provides a hitherto previously absent expert consensus on the current position of health promotion and health education, in nursing and predictions for their future course. Its findings represent an important step for nurses as they seek to become increasingly active and influential within wider health promotion and health education arenas. Relevance to clinical practice. Delphi studies do not necessarily offer indisputable fact. This study, however, with its strong consensus on the majority of original statements is a good indicator as to how nursing experts currently view health promotion and health education constructs. Expert consensus offers a useful form of measure against current and future clinical practice and helps to build a firm foundation for change. Nurses, then, are advised here to refer to the findings presented, that they remain contextually and conceptually clear, as they embark on current and future health promotion-related activities.

Technical Progress of the New Worlds Observer Mission

NASA Astrophysics Data System (ADS)

Lo, Amy; Noecker, C.; Cash, W.; NWO Study Team

2009-01-01

We report on the technical progress of the New Worlds Observer (NWO) mission concept. NWO is a two spacecraft mission that is capable of detecting and characterizing extra-solar, terrestrial planets and planetary systems. NWO consists of an external starshade and an UV-optical space telescope, flying in tandem. The starshade is a petal-shaped, opaque screen that creates an extremely dark shadow large enough to shade the telescope aperture from the target star. The NWO team has been addressing the top technology challenges of the concept, and report here our progress. We will present the current mission configuration best suited to address Terrestrial Planet Finding requirements, and highlight the technological breakthroughs that we have achieved this year. In particular, we will report on progress made in precision deployables for the large starshade, and the trajectory & alignment control system for NWO. We will also briefly highlight advances in understanding the starshade optical performance.

Matching disease and phenotype ontologies in the ontology alignment evaluation initiative.

PubMed

Harrow, Ian; Jiménez-Ruiz, Ernesto; Splendiani, Andrea; Romacker, Martin; Woollard, Peter; Markel, Scott; Alam-Faruque, Yasmin; Koch, Martin; Malone, James; Waaler, Arild

2017-12-02

The disease and phenotype track was designed to evaluate the relative performance of ontology matching systems that generate mappings between source ontologies. Disease and phenotype ontologies are important for applications such as data mining, data integration and knowledge management to support translational science in drug discovery and understanding the genetics of disease. Eleven systems (out of 21 OAEI participating systems) were able to cope with at least one of the tasks in the Disease and Phenotype track. AML, FCA-Map, LogMap(Bio) and PhenoMF systems produced the top results for ontology matching in comparison to consensus alignments. The results against manually curated mappings proved to be more difficult most likely because these mapping sets comprised mostly subsumption relationships rather than equivalence. Manual assessment of unique equivalence mappings showed that AML, LogMap(Bio) and PhenoMF systems have the highest precision results. Four systems gave the highest performance for matching disease and phenotype ontologies. These systems coped well with the detection of equivalence matches, but struggled to detect semantic similarity. This deserves more attention in the future development of ontology matching systems. The findings of this evaluation show that such systems could help to automate equivalence matching in the workflow of curators, who maintain ontology mapping services in numerous domains such as disease and phenotype.

miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments

PubMed Central

Hackenberg, Michael; Rodríguez-Ezpeleta, Naiara; Aransay, Ana M.

2011-01-01

We present a new version of miRanalyzer, a web server and stand-alone tool for the detection of known and prediction of new microRNAs in high-throughput sequencing experiments. The new version has been notably improved regarding speed, scope and available features. Alignments are now based on the ultrafast short-read aligner Bowtie (granting also colour space support, allowing mismatches and improving speed) and 31 genomes, including 6 plant genomes, can now be analysed (previous version contained only 7). Differences between plant and animal microRNAs have been taken into account for the prediction models and differential expression of both, known and predicted microRNAs, between two conditions can be calculated. Additionally, consensus sequences of predicted mature and precursor microRNAs can be obtained from multiple samples, which increases the reliability of the predicted microRNAs. Finally, a stand-alone version of the miRanalyzer that is based on a local and easily customized database is also available; this allows the user to have more control on certain parameters as well as to use specific data such as unpublished assemblies or other libraries that are not available in the web server. miRanalyzer is available at http://bioinfo2.ugr.es/miRanalyzer/miRanalyzer.php. PMID:21515631

Enhancing nutrition with pulses: defining a recommended serving size for adults

PubMed Central

Marinangeli, Christopher P F; Curran, Julianne; Barr, Susan I; Slavin, Joanne; Puri, Seema; Swaminathan, Sumathi; Tapsell, Linda; Patterson, Carol Ann

2017-01-01

Abstract Pulses, defined as dry-harvested leguminous crops, include several varieties of beans, peas, lentils, and chickpeas. There is no consensus around a recommended serving size of pulses within a balanced diet, which prevents the development of transregional strategies that rely on consistent messaging to drive increases in consumption. The purpose of this review is to define and disseminate an appropriate target for a minimum serving size of pulses on any given day that can be used in international or collaborative strategies to promote the consumption of pulses. Relevant data were reviewed to examine dietary guidelines across jurisdictions, determine consumption levels of pulses across the globe, evaluate the nutritional composition of pulses in the context of dietary nutrient insufficiency, and assess the impact of pulses on dietary quality. Across a variety of pulses, 100 g of cooked pulses aligned with most regional serving sizes for pulses and provides significant levels of nutrients that are underconsumed by specific age-sex groups. Moreover, 100 g of pulses provides a number of nutrients that qualify for nutrient content claims under regional regulatory frameworks. The data demonstrate that 100 g or 125 mL (0.5 metric cup) of cooked pulses is a reasonable target for aligning strategies that promote the dietary and nutritional attributes of these legumes. PMID:29202192

Learning about and from others' prudence, impatience or laziness: The computational bases of attitude alignment.

PubMed

Devaine, Marie; Daunizeau, Jean

2017-03-01

Peoples' subjective attitude towards costs such as, e.g., risk, delay or effort are key determinants of inter-individual differences in goal-directed behaviour. Thus, the ability to learn about others' prudent, impatient or lazy attitudes is likely to be critical for social interactions. Conversely, how adaptive such attitudes are in a given environment is highly uncertain. Thus, the brain may be tuned to garner information about how such costs ought to be arbitrated. In particular, observing others' attitude may change one's uncertain belief about how to best behave in related difficult decision contexts. In turn, learning from others' attitudes is determined by one's ability to learn about others' attitudes. We first derive, from basic optimality principles, the computational properties of such a learning mechanism. In particular, we predict two apparent cognitive biases that would arise when individuals are learning about others' attitudes: (i) people should overestimate the degree to which they resemble others (false-consensus bias), and (ii) they should align their own attitudes with others' (social influence bias). We show how these two biases non-trivially interact with each other. We then validate these predictions experimentally by profiling people's attitudes both before and after guessing a series of cost-benefit arbitrages performed by calibrated artificial agents (which are impersonating human individuals).

Learning about and from others' prudence, impatience or laziness: The computational bases of attitude alignment

PubMed Central

Devaine, Marie

2017-01-01

Peoples' subjective attitude towards costs such as, e.g., risk, delay or effort are key determinants of inter-individual differences in goal-directed behaviour. Thus, the ability to learn about others' prudent, impatient or lazy attitudes is likely to be critical for social interactions. Conversely, how adaptive such attitudes are in a given environment is highly uncertain. Thus, the brain may be tuned to garner information about how such costs ought to be arbitrated. In particular, observing others' attitude may change one's uncertain belief about how to best behave in related difficult decision contexts. In turn, learning from others' attitudes is determined by one's ability to learn about others' attitudes. We first derive, from basic optimality principles, the computational properties of such a learning mechanism. In particular, we predict two apparent cognitive biases that would arise when individuals are learning about others’ attitudes: (i) people should overestimate the degree to which they resemble others (false-consensus bias), and (ii) they should align their own attitudes with others’ (social influence bias). We show how these two biases non-trivially interact with each other. We then validate these predictions experimentally by profiling people's attitudes both before and after guessing a series of cost-benefit arbitrages performed by calibrated artificial agents (which are impersonating human individuals). PMID:28358869

Design and development of progressive tool for manufacturing washer

NASA Astrophysics Data System (ADS)

Annigeri, Ulhas K.; Raghavendra Ravi Kiran, K.; Deepthi, Y. P.

2017-07-01

In a progressive tool the raw material is worked at different station to finally fabricate the component. A progressive tool is a lucrative tool for mass production of components. A lot of automobile and other transport industries develop progressive tool for the production of components. The design of tool involves lot of planning and the same amount of skill of process planning is required in the fabrication of the tool. The design also involves use of thumb rules and standard elements as per experience gained in practice. Manufacturing the press tool is a laborious task as special jigs and fixtures have to be designed for the purpose. Assembly of all the press tool elements is another task where use of accurate measuring instruments for alignment of various tool elements is important. In the present study, design and fabrication of progressive press tool for production of washer has been developed and the press tool has been tried out on a mechanical type of press. The components produced are to dimensions.

Recommendations for initiation and cessation of enzyme replacement therapy in patients with Fabry disease: the European Fabry Working Group consensus document.

PubMed

Biegstraaten, Marieke; Arngrímsson, Reynir; Barbey, Frederic; Boks, Lut; Cecchi, Franco; Deegan, Patrick B; Feldt-Rasmussen, Ulla; Geberhiwot, Tarekegn; Germain, Dominique P; Hendriksz, Chris; Hughes, Derralynn A; Kantola, Ilkka; Karabul, Nesrin; Lavery, Christine; Linthorst, Gabor E; Mehta, Atul; van de Mheen, Erica; Oliveira, João P; Parini, Rossella; Ramaswami, Uma; Rudnicki, Michael; Serra, Andreas; Sommer, Claudia; Sunder-Plassmann, Gere; Svarstad, Einar; Sweeb, Annelies; Terryn, Wim; Tylki-Szymanska, Anna; Tøndel, Camilla; Vujkovac, Bojan; Weidemann, Frank; Wijburg, Frits A; Woolfson, Peter; Hollak, Carla E M

2015-03-27

Fabry disease (FD) is a lysosomal storage disorder resulting in progressive nervous system, kidney and heart disease. Enzyme replacement therapy (ERT) may halt or attenuate disease progression. Since administration is burdensome and expensive, appropriate use is mandatory. We aimed to define European consensus recommendations for the initiation and cessation of ERT in patients with FD. A Delphi procedure was conducted with an online survey (n = 28) and a meeting (n = 15). Patient organization representatives were present at the meeting to give their views. Recommendations were accepted with ≥75% agreement and no disagreement. For classically affected males, consensus was achieved that ERT is recommended as soon as there are early clinical signs of kidney, heart or brain involvement, but may be considered in patients of ≥16 years in the absence of clinical signs or symptoms of organ involvement. Classically affected females and males with non-classical FD should be treated as soon as there are early clinical signs of kidney, heart or brain involvement, while treatment may be considered in females with non-classical FD with early clinical signs that are considered to be due to FD. Consensus was achieved that treatment should not be withheld from patients with severe renal insufficiency (GFR < 45 ml/min/1.73 m(2)) and from those on dialysis or with cognitive decline, but carefully considered on an individual basis. Stopping ERT may be considered in patients with end stage FD or other co-morbidities, leading to a life expectancy of <1 year. In those with cognitive decline of any cause, or lack of response for 1 year when the sole indication for ERT is neuropathic pain, stopping ERT may be considered. Also, in patients with end stage renal disease, without an option for renal transplantation, in combination with advanced heart failure (NYHA class IV), cessation of ERT should be considered. ERT in patients who are non-compliant or fail to attend regularly at visits should be stopped. The recommendations can be used as a benchmark for initiation and cessation of ERT, although final decisions should be made on an individual basis. Future collaborative efforts are needed for optimization of these recommendations.

Toward Large-Area Sub-Arcsecond X-Ray Telescopes

NASA Technical Reports Server (NTRS)

O'Dell, Stephen L.; Aldcroft, Thomas L.; Allured, Ryan; Atkins, Carolyn; Burrows, David N.; Cao, Jian; Chalifoux, Brandon D.; Chan, Kai-Wing; Cotroneo, Vincenzo; Elsner, Ronald F.;

Development of an active behavioural physiotherapy intervention (ABPI) for acute whiplash-associated disorder (WAD) II management: a modified Delphi study.

PubMed

Wiangkham, Taweewat; Duda, Joan; Haque, M Sayeed; Rushton, Alison

2016-09-14

To develop an active behavioural physiotherapy intervention (ABPI) for managing acute whiplash-associated disorder (WAD) II using a modified Delphi method to develop consensus for the basic features of the ABPI. Modified Delphi study. Our systematic review and meta-analysis evaluating conservative management for acute WADII found that a combined ABPI may be a useful intervention to prevent patients progressing to chronicity. No previous research has considered a combined behavioural approach and active physiotherapy in the management of acute WADII patients. The ABPI was therefore developed using a rigorous consensus method using international research and local clinical whiplash experts. Descriptive statistics were used to assess consensus in each round. Online international survey. A purposive sample of 97 potential participants (aiming to recruit n=30) consisting of international research whiplash experts, UK private physiotherapists and UK postgraduate musculoskeletal physiotherapy students were invited to participate via electronic mail with an attached participant information sheet and consent form. 36 individuals signed and returned the consent form. In round 1, 32/36 participants (response rate=89%, mean age±SD=36.03±13.22 years) across 8 countries (Australia, Finland, Greece, India, Netherlands, Norway, Sweden and UK) contributed to round 1 questionnaire. Response rates were 78% and 75% for rounds 2 and 3, respectively. Following round 3, 12 underlying principles (eg, return to normal function as soon as possible, pain management, encouragement of self-management, reduce fear avoidance and anxiety) achieved consensus. The treatment components reaching consensus included behavioural (eg, education, reassurance, self-management) and physiotherapy components (eg, exercises for stability and mobility). No passive intervention achieved consensus. Experts suggested and agreed the underlying principles and treatment components of the ABPI for the management of acute WADII. The ABPI was underpinned by social cognitive theory focusing on self-efficacy enhancement prior to conducting a phase II trial. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Primary intracranial soft tissue sarcomas in children, adolescents, and young adults: single institution experience and review of the literature.

PubMed

Maher, Ossama M; Khatua, Soumen; Mukherjee, Devashis; Olar, Adriana; Lazar, Alexander; Luthra, Raja; Liu, Diane; Wu, Jimin; Ketonen, Leena; Zaky, Wafik

2016-03-01

There is a paucity of literature reporting the outcome of intracranial sarcomas (IS) in children, adolescents, and young adults (CAYA). A multimodal therapeutic approach is commonly used, with no well-established treatment consensus. We conducted a retrospective review of CAYA with IS, treated at our institution, to determine their clinical findings, treatments, and outcomes. Immunohistochemistry (PDGFRA and EGFR) and DNA sequencing were performed on 5 tumor samples. A literature review of IS was also conducted. We reviewed 13 patients (median age, 7 years) with a primary diagnosis of IS between 1990 and 2015. Diagnoses included unclassified sarcoma (n = 9), chondrosarcoma (n = 2), and rhabdomyosarcoma (n = 2). Five patients underwent upfront gross total resection (GTR) of the tumor. The 5-drug regimen (vincristine, doxorubicin, cyclophosphamide, etoposide, and ifosfamide) was the most common treatment used. Nine patients died due to progression or recurrence (n = 8) or secondary malignancy (n = 1). The median follow-up period of the 4 surviving patients was 1.69 years (range 1.44-5.17 years). The 5-year progression-free survival and overall survival rates were 21 and 44 %, respectively. BRAF, TP53, KRAS, KIT, ERBB2, MET, RET, ATM, and EGFR mutations were detected in 4 of the 5 tissue samples. All 5 samples were immunopositive for PDGFRA, and only 2 were positive for EGFR. IS remain a therapeutic challenge due to high progression and recurrence rates. Collaborative multi-institutional studies are warranted to delineate a treatment consensus and investigate tumor biology to improve the disease outcome.

Outcomes of hip resurfacing in a professional dancer: a case report.

PubMed

Dunleavy, Kim

2012-02-01

A new surgical option (hip resurfacing arthroplasty) is now available for younger patients with hip osteoarthritis. A more aggressive rehabilitation program than the typical total hip arthroplasty protocol is needed for active individuals. This case report describes interventions used to maximize function in a 46-year-old professional dancer after hip resurfacing with a progressive therapeutic exercise program. Exercise choices were selected to address dance-specific requirements while respecting healing of the posterior capsular incision. Strengthening focused on hip abduction, extension, and external rotation. Precautions included avoiding gluteal stretching until 6 months. Pelvic alignment and weight-bearing distribution were emphasized. The patient was able to return to rehearsal by 7 months, at which time strength was equivalent to the unaffected leg. Range of motion reached unaffected side values at week 8 for internal rotation, week 11 for extension, week 13 for adduction, and week 28 for flexion. External rotation and abduction were still limited at 1 year, which influenced pelvic alignment with resultant pain on the unaffected side. Functional and impairment outcomes are presented with timelines to provide a basis for postoperative benchmarks for active clients after hip resurfacing. Although this case report presents a dance-specific program, exercise progressions for other active individuals may benefit from similar exercise intensity and sports-specific focus. Future rehabilitation programs should take into account possible flexion and external rotation range limitations and the need for gluteal muscle strengthening along with symmetry and pelvic alignment correction. Long-term studies investigating intensity of rehabilitation are warranted for patients intending to participate in higher level athletic activity.

Prognostic Factors in the Midterm Results of Pullout Fixation for Posterior Root Tears of the Medial Meniscus.

PubMed

Chung, Kyu Sung; Ha, Jeong Ku; Ra, Ho Jong; Kim, Jin Goo

2016-07-01

To identify predictors of unfavorable clinical and radiologic outcomes a minimum of 5 years after pullout fixation for medial meniscus posterior root tears (MMPRTs). In total, 40 patients who were followed for >5 years after pullout fixation in MMPRT were recruited. The mean follow-up duration was 71.1 months. Clinical outcomes, including Lysholm score and International Knee Documentation Committee (IKDC) score, and radiographic results, including Kellgren-Lawrence (K-L; 0/1/2/3/4) grade and medial joint space width, were evaluated preoperatively and at final follow-up. Preoperative prognostic factors, including age, sex, body mass index, degree of varus alignment, K-L grade, medial joint space width, meniscal extrusion, and cartilage status, by the modified Outerbridge classification (grades 1 or 2 v 3 or 4), for relatively unfavorable (fair or poor grade) Lysholm or IKDC score, and progression of K-L grade were investigated by multivariate logistic regression analysis. The mean Lysholm score (52.1 ± 8.8 to 83.8 ± 11.9) and IKDC score (40.1 ± 7.6 to 73.3 ± 10.9) were improved significantly (P < .001), although the loss of medial joint space width (4.8 ± 1.1 to 3.9 ± 1.1 mm) and K-L grade (6/25/9/0/0 to 0/11/20/9/0) progressed significantly (P < .001). Unfavorable prognostic factors of the Lysholm score were grade ≥3 chondral lesions (odds ratio [OR] = 5.993; P = .028) and varus mechanical alignment (OR = 1.644; P = .017), for IKDC score were grade ≥3 chondral lesions (OR = 11.146; P = .038) and older age (OR = 1.200; P = .017). Preoperative chondral lesion grade ≥3 increased the risk of K-L grade progression (OR = 11.000; P = .031). Clinically, modified Outerbridge classification grade ≥3 chondral lesions, varus alignment, and older age were found to predict a poor prognosis after MMPRT fixation. In terms of radiographic K-L grade progression, grade ≥3 chondral lesions were identified as a poor prognostic factor. Level IV, case series. Copyright © 2016 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

The wisdom of the commons: ensemble tree classifiers for prostate cancer prognosis

PubMed Central

Koziol, James A.; Feng, Anne C.; Jia, Zhenyu; Wang, Yipeng; Goodison, Seven; McClelland, Michael; Mercola, Dan

2009-01-01

Motivation: Classification and regression trees have long been used for cancer diagnosis and prognosis. Nevertheless, instability and variable selection bias, as well as overfitting, are well-known problems of tree-based methods. In this article, we investigate whether ensemble tree classifiers can ameliorate these difficulties, using data from two recent studies of radical prostatectomy in prostate cancer. Results: Using time to progression following prostatectomy as the relevant clinical endpoint, we found that ensemble tree classifiers robustly and reproducibly identified three subgroups of patients in the two clinical datasets: non-progressors, early progressors and late progressors. Moreover, the consensus classifications were independent predictors of time to progression compared to known clinical prognostic factors. Contact: dmercola@uci.edu PMID:18628288

[The current state and prospect of Chinese medicine gastroenterology].

PubMed

Zhang, Sheng-Sheng; Zhou, Tao

2012-03-01

The progress and existent problems of Chinese medicine (CM) gastroenterology since the National Eleventh Five-Year Plan were discussed in this article in terms of theory innovation, formulation of clinical pathway and diagnosis-treatment consensus, efficacy assessment, formulation of efficacy assessment scale, advantage diseases, and exploration of the syndrome standardization, progress in science research, academic exchange, and the construction of study platform, and so on. Meanwhile, the development of CM gastroenterology was prospected in the following five aspects: to enhance the theory inheritance and innovation, the construction of discipline standardization; to establish scientific clinical efficacy assessment methods and the standard system; to expend treatment technologies and feature therapies; and to clarify the modern scientific connotation of CM theory and treatment.

A consensus for the development of a vector model to assess clinical complexity.

PubMed

Corazza, Gino Roberto; Klersy, Catherine; Formagnana, Pietro; Lenti, Marco Vincenzo; Padula, Donatella

2017-12-01

The progressive rise in multimorbidity has made management of complex patients one of the most topical and challenging issues in medicine, both in clinical practice and for healthcare organizations. To make this easier, a score of clinical complexity (CC) would be useful. A vector model to evaluate biological and extra-biological (socio-economic, cultural, behavioural, environmental) domains of CC was proposed a few years ago. However, given that the variables that grade each domain had never been defined, this model has never been used in clinical practice. To overcome these limits, a consensus meeting was organised to grade each domain of CC, and to establish the hierarchy of the domains. A one-day consensus meeting consisting of a multi-professional panel of 25 people was held at our Hospital. In a preliminary phase, the proponents selected seven variables as qualifiers for each of the five above-mentioned domains. In the course of the meeting, the panel voted for five variables considered to be the most representative for each domain. Consensus was established with 2/3 agreement, and all variables were dichotomised. Finally, the various domains were parametrized and ranked within a feasible vector model. A Clinical Complexity Index was set up using the chosen variables. All the domains were graphically represented through a vector model: the biological domain was chosen as the most significant (highest slope), followed by the behavioural and socio-economic domains (intermediate slope), and lastly by the cultural and environmental ones (lowest slope). A feasible and comprehensive tool to evaluate CC in clinical practice is proposed herein.

How Does Student Understanding of a Concept Change Throughout a Unit of Instruction? Support Toward the Theory of Learning Progressions

NASA Astrophysics Data System (ADS)

Dyer, Brian Jay

This study documented the changes in understanding a class of eighth grade high school-level biology students experienced through a biology unit introducing genetics. Learning profiles for 55 students were created using concept maps and interviews as qualitative and quantitative instruments. The study provides additional support to the theory of learning progressions called for by experts in the field. The students' learning profiles were assessed to determine the alignment with a researcher-developed learning profile. The researcher-developed learning profile incorporated the learning progressions published in the Next Generation Science Standards, as well as current research in learning progressions for 5-10th grade students studying genetics. Students were found to obtain understanding of the content in a manner that was nonlinear, even circuitous. This opposes the prevailing interpretation of learning progressions, that knowledge is ascertained in escalating levels of complexity. Learning progressions have implications in teaching sequence, assessment, education research, and policy. Tracking student understanding of other populations of students would augment the body of research and enhance generalizability.

Current progress and technical challenges of flexible liquid crystal displays

NASA Astrophysics Data System (ADS)

Fujikake, Hideo; Sato, Hiroto

2009-02-01

We focused on several technical approaches to flexible liquid crystal (LC) display in this report. We have been developing flexible displays using plastic film substrates based on polymer-dispersed LC technology with molecular alignment control. In our representative devices, molecular-aligned polymer walls keep plastic-substrate gap constant without LC alignment disorder, and aligned polymer networks create monostable switching of fast-response ferroelectric LC (FLC) for grayscale capability. In the fabrication process, a high-viscosity FLC/monomer solution was printed, sandwiched and pressed between plastic substrates. Then the polymer walls and networks were sequentially formed based on photo-polymerization-induced phase separation in the nematic phase by two exposure processes of patterned and uniform ultraviolet light. The two flexible backlight films of direct illumination and light-guide methods using small three-primary-color light-emitting diodes were fabricated to obtain high-visibility display images. The fabricated flexible FLC panels were driven by external transistor arrays, internal organic thin film transistor (TFT) arrays, and poly-Si TFT arrays. We achieved full-color moving-image displays using the flexible FLC panel and the flexible backlight film based on field-sequential-color driving technique. Otherwise, for backlight-free flexible LC displays, flexible reflective devices of twisted guest-host nematic LC and cholesteric LC were discussed with molecular-aligned polymer walls. Singlesubstrate device structure and fabrication method using self-standing polymer-stabilized nematic LC film and polymer ceiling layer were also proposed for obtaining LC devices with excellent flexibility.

Fifth Ovarian Cancer Consensus Conference of the Gynecologic Cancer InterGroup: Recommendations on incorporating patient-reported outcomes in clinical trials in epithelial ovarian cancer.

PubMed

Joly, Florence; Hilpert, Felix; Okamoto, Aikou; Stuart, Gavin; Ochiai, Kasunori; Friedlander, Michael

2017-06-01

Despite the support for including patient-reported outcomes (PROs) and health-related quality of life in clinical trials, there have been deficiencies in how these have been assessed and reported in epithelial ovarian cancer (EOC) clinical trials. To redress this, the 5th Ovarian Cancer Consensus Conference, included a plenary session entitled 'How to include PROs in clinical trials'. The perspective is a summary of the recommendations made by the Gynecologic Cancer InterGroup unanimously agreed on the importance of PROs and PRO end-points in EOC clinical trials. They recognised that effort must be made to ensure the integrity of collection of PRO data and to avoid missing data. PRO end-points should be based on the PRO hypotheses, be context specific and reflect the patient population and the objectives of treatment (e.g. first line, maintenance therapy, early or late relapse). The PRO end-points inform the choice of PRO measures used in the trial and how the results are analysed and reported. There was agreement that progression-free survival should be supported by PROs among patients with late relapse (platinum sensitive) and that progression-free survival alone was not sufficient as the primary end-point of clinical trials in patients with platinum resistant/refractory EOC and PROs should be included as either the primary/co-primary end-point in this subset of patients. Novel approaches to measure the benefit of palliative chemotherapy such as time until definitive deterioration of Health-Related Quality of Life were recommended. There was consensus to endorse the ISOQOL and CONSORT-PRO guidelines on the inclusion and reporting of PRO endpoints in protocols and that all future EOC Gynecologic Cancer InterGroup trials should adhere to these. Copyright © 2017 Elsevier Ltd. All rights reserved.

Cognitive and adaptive measurement endpoints for clinical trials in mucopolysaccharidoses types I, II, and III: A review of the literature.

PubMed

Janzen, Darren; Delaney, Kathleen A; Shapiro, Elsa G

2017-06-01

Sensitive, reliable measurement instruments are critical for the evaluation of disease progression and new treatments that affect the brain in the mucopolysaccharidoses (MPS). MPS I, II, and III have early onset clinical phenotypes that affect the brain during development and result in devastating cognitive decline and ultimately death without treatment. Comparisons of outcomes are hindered by diverse protocols and approaches to assessment including applicability to international trials necessary in rare diseases. We review both cognitive and adaptive measures with the goal of providing evidence to a Delphi panel to come to a consensus about recommendations for clinical trials for various age groups. The results of the consensus panel are reported in an accompanying article. The following data were gathered (from internet resources and from test manuals) for each measure and summarized in the discussion: reliability, validity, date and adequacy of normative data, applicability of the measure's metrics, cross cultural validity including translations and adaptations, feasibility in the MPS population, familiarity to sites, sensitivity to change, and interpretability. If, resulting from this consensus, standard protocols are used for both natural history and treatment studies, patients, their families, and health care providers will benefit from the ability to compare study outcomes. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Maximizing the sensitivity and reliability of peptide identification in large-scale proteomic experiments by harnessing multiple search engines.

PubMed

Yu, Wen; Taylor, J Alex; Davis, Michael T; Bonilla, Leo E; Lee, Kimberly A; Auger, Paul L; Farnsworth, Chris C; Welcher, Andrew A; Patterson, Scott D

2010-03-01

Despite recent advances in qualitative proteomics, the automatic identification of peptides with optimal sensitivity and accuracy remains a difficult goal. To address this deficiency, a novel algorithm, Multiple Search Engines, Normalization and Consensus is described. The method employs six search engines and a re-scoring engine to search MS/MS spectra against protein and decoy sequences. After the peptide hits from each engine are normalized to error rates estimated from the decoy hits, peptide assignments are then deduced using a minimum consensus model. These assignments are produced in a series of progressively relaxed false-discovery rates, thus enabling a comprehensive interpretation of the data set. Additionally, the estimated false-discovery rate was found to have good concordance with the observed false-positive rate calculated from known identities. Benchmarking against standard proteins data sets (ISBv1, sPRG2006) and their published analysis, demonstrated that the Multiple Search Engines, Normalization and Consensus algorithm consistently achieved significantly higher sensitivity in peptide identifications, which led to increased or more robust protein identifications in all data sets compared with prior methods. The sensitivity and the false-positive rate of peptide identification exhibit an inverse-proportional and linear relationship with the number of participating search engines.

[Consensus document for the detection and management of chronic kidney disease].

PubMed

Martínez-Castelao, Alberto; Górriz, José L; Bover, Jordi; Segura-de la Morena, Julián; Cebollada, Jesús; Escalada, Javier; Esmatjes, Enric; Fácila, Lorenzo; Gamarra, Javier; Gràcia, Silvia; Hernández-Moreno, Julio; Llisterri-Caro, José L; Mazón, Pilar; Montañés, Rosario; Morales-Olivas, Francisco; Muñoz-Torres, Manuel; de Pablos-Velasco, Pedro; de Santiago, Ana; Sánchez-Celaya, Marta; Suárez, Carmen; Tranche, Salvador

2014-11-01

Chronic kidney disease (CKD) is an important global health problem, involving to 10% of the Spanish population, promoting high morbidity and mortality for the patient and an elevate consumption of the total health resources for the National Health System. This is a summary of an executive consensus document of ten scientific societies involved in the care of the renal patient, that actualizes the consensus document published in 2007. The central extended document can be consulted in the web page of each society. The aspects included in the document are: Concept, epidemiology and risk factors for CKD. Diagnostic criteria, evaluation and stages of CKD, albuminuria and glomerular filtration rate estimation. Progression factors for renal damage. Patient remission criteria. Follow-up and objectives of each speciality control. Nephrotoxicity prevention. Cardio-vascular damage detection. Diet, life-style and treatment attitudes: hypertension, dyslipidaemia, hyperglycemia, smoking, obesity, hyperuricemia, anemia, mineral and bone disorders. Multidisciplinary management for Primary Care, other specialities and Nephrology. Integrated management of CKD patient in haemodialysis, peritoneal dialysis and renal transplant patients. Management of the uremic patient in palliative care. We hope that this document may be of help for the multidisciplinary management of CKD patients by summarizing the most updated recommendations. Copyright © 2014 Elsevier España, S.L.U. All rights reserved.

[Consensus document for the detection and management of chronic kidney disease].

PubMed

Martínez-Castelao, Alberto; Górriz, José L; Bover, Jordi; Segura-de la Morena, Julián; Cebollada, Jesús; Escalada, Javier; Esmatjes, Enric; Fácila, Lorenzo; Gamarra, Javier; Gràcia, Silvia; Hernández-Moreno, Julio; Llisterri-Caro, José L; Mazón, Pilar; Montañés, Rosario; Morales-Olivas, Francisco; Muñoz-Torres, Manuel; de Pablos-Velasco, Pedro; de Santiago, Ana; Sánchez-Celaya, Marta; Suárez, Carmen; Tranche, Salvador

2014-11-01

Chronic kidney disease (CKD) is an important global health problem, involving to 10% of the Spanish population, promoting high morbidity and mortality for the patient and an elevate consumption of the total health resources for the National Health System. This is a summary of an executive consensus document of ten scientific societies involved in the care of the renal patient, that actualizes the consensus document published in 2007. The central extended document can be consulted in the web page of each society. The aspects included in the document are: Concept, epidemiology and risk factors for CKD. Diagnostic criteria, evaluation and stages of CKD, albuminuria and glomerular filtration rate estimation. Progression factors for renal damage. Patient remission criteria. Follow-up and objectives of each speciality control. Nephrotoxicity prevention. Cardio-vascular damage detection. Diet, life-style and treatment attitudes: hypertension, dyslipidaemia, hyperglycemia, smoking, obesity, hyperuricemia, anemia, mineral and bone disorders. Multidisciplinary management for Primary Care, other specialities and Nephrology. Integrated management of CKD patient in haemodialysis, peritoneal dialysis and renal transplant patients. Management of the uremic patient in palliative care. We hope that this document may be of help for the multidisciplinary management of CKD patients by summarizing the most updated recommendations. Copyright © 2014. Published by Elsevier Espana.

Harmonized clinical trial methodologies for localized cutaneous leishmaniasis and potential for extensive network with capacities for clinical evaluation

PubMed Central

Grogl, Max; Boni, Marina; Carvalho, Edgar M.; Chebli, Houda; Cisse, Mamoudou; Diro, Ermias; Fernandes Cota, Gláucia; Erber, Astrid C.; Gadisa, Endalamaw; Handjani, Farhad; Khamesipour, Ali; Llanos-Cuentas, Alejandro; López Carvajal, Liliana; Grout, Lise; Lmimouni, Badre Eddine; Mokni, Mourad; Nahzat, Mohammad Sami; Ben Salah, Afif; Ozbel, Yusuf; Pascale, Juan Miguel; Rizzo Molina, Nidia; Rode, Joelle; Romero, Gustavo; Ruiz-Postigo, José Antonio; Gore Saravia, Nancy; Soto, Jaime; Uzun, Soner; Mashayekhi, Vahid; Vélez, Ivan Dario; Vogt, Florian; Zerpa, Olga; Arana, Byron

2018-01-01

Introduction Progress with the treatment of cutaneous leishmaniasis (CL) has been hampered by inconsistent methodologies used to assess treatment effects. A sizable number of trials conducted over the years has generated only weak evidence backing current treatment recommendations, as shown by systematic reviews on old-world and new-world CL (OWCL and NWCL). Materials and methods Using a previously published guidance paper on CL treatment trial methodology as the reference, consensus was sought on key parameters including core eligibility and outcome measures, among OWCL (7 countries, 10 trial sites) and NWCL (7 countries, 11 trial sites) during two separate meetings. Results Findings and level of consensus within and between OWCL and NWCL sites are presented and discussed. In addition, CL trial site characteristics and capacities are summarized. Conclusions The consensus reached allows standardization of future clinical research across OWCL and NWCL sites. We encourage CL researchers to adopt and adapt as required the proposed parameters and outcomes in their future trials and provide feedback on their experience. The expertise afforded between the two sets of clinical sites provides the basis for a powerful consortium with potential for extensive, standardized assessment of interventions for CL and faster approval of candidate treatments. PMID:29329311

COPD control: Can a consensus be found?

PubMed

Guimarães, M; Bugalho, A; Oliveira, A S; Moita, J; Marques, A

2016-01-01

There are currently no reliable instruments for assessing the onset and progression of chronic obstructive pulmonary disease (COPD) or predicting its prognosis. Currently, a comprehensive assessment of COPD including several objective and subjective parameters is recommended. However, the lack of biomarkers precludes a correct assessment of COPD severity, which consequently hampers adequate therapeutic approaches and COPD control. In the absence of a definition of "well-controlled disease", a consensus regarding COPD control will be difficult to reach. However, COPD patient assessment should be multidimensional, and anchored in five points: control of symptoms, decline of pulmonary function, levels of physical activity, exacerbations, and Quality of Life. Several non-pharmacological and pharmacological measures are currently available to achieve disease control. Smoking cessation, vaccination, exercise training programs and pulmonary rehabilitation are recognized as important non-pharmacological measures but bronchodilators are the pivotal therapy in the control of COPD. This paper discusses several objective and subjective parameters that may bridge the gap between disease assessment and disease control. The authors conclude that, at present, it is not possible to reach a consensus regarding COPD control, essentially due to the lack of objective instruments to measure it. Some recommendations are set forth, but true COPD control awaits further objective assessments. Copyright © 2016. Published by Elsevier España, S.L.U.

First European consensus for diagnosis, management, and treatment of transthyretin familial amyloid polyneuropathy

PubMed Central

Adams, David; Suhr, Ole B.; Hund, Ernst; Obici, Laura; Tournev, Ivailo; Campistol, Josep M.; Slama, Michel S.; Hazenberg, Bouke P.; Coelho, Teresa

2016-01-01

Purpose of review Early and accurate diagnosis of transthyretin familial amyloid polyneuropathy (TTR-FAP) represents one of the major challenges faced by physicians when caring for patients with idiopathic progressive neuropathy. There is little consensus in diagnostic and management approaches across Europe. Recent findings The low prevalence of TTR-FAP across Europe and the high variation in both genotype and phenotypic expression of the disease means that recognizing symptoms can be difficult outside of a specialized diagnostic environment. The resulting delay in diagnosis and the possibility of misdiagnosis can misguide clinical decision-making and negatively impact subsequent treatment approaches and outcomes. Summary This review summarizes the findings from two meetings of the European Network for TTR-FAP (ATTReuNET). This is an emerging group comprising representatives from 10 European countries with expertise in the diagnosis and management of TTR-FAP, including nine National Reference Centres. The current review presents management strategies and a consensus on the gold standard for diagnosis of TTR-FAP as well as a structured approach to ongoing multidisciplinary care for the patient. Greater communication, not just between members of an individual patient's treatment team, but also between regional and national centres of expertise, is the key to the effective management of TTR-FAP. PMID:26734952

Diamond-anvil high-pressure cell with improved X-ray collimation system

DOEpatents

Schiferl, David; Olinger, Barton W.; Livingston, Robert W.

1986-01-01

An adjustable X-ray collimation system for a diamond-anvil high-pressure cell of the type including a cooperable piston and cylinder and a pair of opposing diamonds located between the head of the piston and the head of the cylinder. The X-ray collimation system includes a tubular insert which contains an X-ray collimator. The insert is engageable in the bore of the piston. The collimator is mounted within the insert by means of an elastomeric O-ring at the end closest the opposed diamonds, and by means of a set of adjustable set screws at the opposite end. By adjustment of the set screws the collimator can be pivoted about the O-ring and brought into alignment with the opposed diamonds and the sample contained therein. In the preferred embodiment there is further provided a set of plugs which are insertable in the bore of the collimator. The plugs have bores of different diameters. By successively inserting plugs of progressively smaller bore diameters and adjusting the alignment of the collimator with each plug, the collimator can be quickly brought into accurate alignment with the diamonds. The collimation system allows alignment of the collimator either before or after the cell has been loaded and pressurized.

Strategies and Lessons-Learned for the Successful Alignment of Contract Cost with the Contract Budget Base (CBB) within the First Year of Contract Award - 13154

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

Mullis, Jay; Rueter, Ken

2013-07-01

In order to provide a sound basis and foundation for integrated Project and Contract change management, it is imperative to ensure the alignment of the Negotiated Contract Costs (NCC) with the Contract Budget Base (CBB), where CBB is defined as the Performance Measurement Baseline (PMB) plus Management Reserve (MR). The achievement of this alignment assures customer and contractor agreement on scope, requirements, quantities, schedule and cost, which facilitates the identification of change conditions and ultimate agreement on the value of changes to the NCC and the CBB. Delays in contract/CBB true up/reconciliation can negatively effect measurement of project progress, limitingmore » owner understanding of liability, and may result in increased contract disagreements and potential claims. The Department of Energy Oak Ridge Office of Environmental Management (OR-EM) and URS - CH2M Oak Ridge LLC (UCOR) achieved alignment of the NCC with the CBB within 10 months of UCOR taking over work on the East Tennessee Technology Park (ETTP) cleanup contract by: 1. Managing as a discrete project; 2. Establishing expectations and setting tone of interactions; 3. Using personnel experienced with Federal Acquisition Regulation (FAR); 4. Partnering; 5. Establishing ombudsmen. (authors)« less

Diamond-anvil high-pressure cell with improved x-ray collimation system

DOEpatents

Schiferl, D.; Olinger, B.W.; Livingston, R.W.

1984-03-30

An adjustable x-ray collimation system for a diamond-anvil high-pressure cell of the type including a cooperable piston and cylinder and a pair of opposing diamonds located between the head of the piston and the head of the cylinder. The x-ray collimation system includes a tubular insert which contains an x-ray collimator. The insert is engageable in the bore of the piston. The collimator is mounted within the insert by means of an elastomeric o-ring at the end closest the opposed diamonds, and by means of a set of adjustable set screws at the opposite end. By adjustment of the set screws the collimator can be pivoted about the o-ring and brought into alignment with the opposed diamonds and the sample contained therein. In the preferred embodiment there is further provided a set of plugs which are insertable in the bore of the collimator. The plugs have bores of different diameters. By successively inserting plugs of progressively smaller bore diameters and adjusting the alignment of the collimator with each plug, the collimator can be quickly brought into accurate alignment with the diamonds. The collimation system allows alignment of the collimator either before or after the cell has been loaded and pressurized.

Frontiers of controlling energy levels at interfaces

NASA Astrophysics Data System (ADS)

Koch, Norbert

The alignment of electron energy levels at interfaces between semiconductors, dielectrics, and electrodes determines the function and efficiency of all electronic and optoelectronic devices. Reliable guidelines for predicting the level alignment for a given material combination and methods to adjust the intrinsic energy landscape are needed to enable efficient engineering approaches. These are sufficiently understood for established electronic materials, e.g., Si, but for the increasing number of emerging materials, e.g., organic and 2D semiconductors, perovskites, this is work in progress. The intrinsic level alignment and the underlying mechanisms at interfaces between organic and inorganic semiconductors are discussed first. Next, methods to alter the level alignment are introduced, which all base on proper charge density rearrangement at a heterojunction. As interface modification agents we use molecular electron acceptors and donors, as well as molecular photochromic switches that add a dynamic aspect and allow device multifunctionality. For 2D semiconductors surface transfer doping with molecular acceptors/donors transpires as viable method to locally tune the Fermi-level position in the energy gap. The fundamental electronic properties of a prototypical 1D interface between intrinsic and p-doped 2D semiconductor regions are derived from local (scanning probe) and area-averaged (photoemission) spectroscopy experiments. Future research opportunities for attaining unsurpassed interface control through charge density management are discussed.

Study of J/ψ spin alignment in proton-proton collisions at s = 200 GeV in the PHENIX experiment at RHIC

NASA Astrophysics Data System (ADS)

Shoji, Kohei

2009-10-01

Non-relativisitic QCD calculations using Color Octet Models (COMs) succeed in describing the production cross section of heavy quarkonia measured by CDF and other experiments. However, these models can not reproduce the experimental data for J/ψ spin alignment (polarization). The understanding of the heavy quarkonium production mechanism cannot proceed without additional experimental measurements. The J/ψ spin alignment is experimentally determined by measuring the decay angular distribution of leptons in the J/ψ center of mass system. The anisotropy in the helicity frame was measured at CDF; however, the necessity of analyzing data with respect to another frame like Collins-Soper was recently discussed because the proper polarization axis which is sensitive to the interesting physics phenomenon is not known well. Moreover, measurements of not only the polar angular distribution but also the azimuthal one are important. Proton-proton collision experiments are in progress at the Relativistic Heavy-Ion Collider (RHIC) at Brookhaven National Laboratory. The PHENIX experiment at RHIC has muon spectrometers which can detect decay muons from J/ψ at forward and backward rapidity, 1.2<|η|<2.2. We present the status of our J/ψ spin alignment study in proton-proton collisions at s = 200 GeV.

Essential medicines for breast cancer in low and middle income countries.

PubMed

Bazargani, Y T; de Boer, A; Schellens, J H M; Leufkens, H G M; Mantel-Teeuwisse, Aukje K

2015-08-18

Breast cancer is the most common type of cancer among women worldwide. In low and middle-income countries (LMICs), appropriate selection of medicines on national essential medicines lists (NEMLs) is a first step towards adequate access to treatment. We studied selection of systemic treatments for breast cancer on NEMLs and assessed its alignment with treatment guidelines for different types of early and advanced breast cancer. Furthermore, influence of country characteristics on the selection was investigated. NEMLs from 75 LMICs were studied for inclusion of all components of therapy in each stage of breast cancer according to international consensus guidelines. The results were then grouped by income level, WHO region and the NEMLs' release date. Non parametric tests were used for statistical analysis. Unlike HER2-targeted therapies (<10%), aromatase inhibitors (12%) and taxanes (28%); tamoxifen and first generation chemotherapeutic regimens (e.g., anthracycline-based regimens) were frequently found in the NEMLs (71-78%). Consequently, all components of treatment for "Luminal A" early breast cancer and non HER2 overexpressed advanced breast cancer were found on the NEMLs of over 70% of countries. However, 40% of the low income countries did not have all the components of therapy for any type of early breast cancer in their NEMLs, and adequate treatment of HER2 overexpressed breast cancer was hardly possible with the current selections. Recent NEMLs were more aligned with the guidelines (p < 0.05). Eastern Mediterranean and African regions less frequently incorporated all components of breast cancer treatment in their NEMLs. Alignment of selection with guidelines' recommendations was inconsistent for different types of early and advanced breast cancer in NEMLs. Regular updates and more attention to clinical guidelines is therefore recommended.

Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver

PubMed Central

Blanquart, François; Golubchik, Tanya; Gall, Astrid; Bakker, Margreet; Bezemer, Daniela; Croucher, Nicholas J; Hall, Matthew; Hillebregt, Mariska; Ratmann, Oliver; Albert, Jan; Bannert, Norbert; Fellay, Jacques; Fransen, Katrien; Gourlay, Annabelle; Grabowski, M Kate; Gunsenheimer-Bartmeyer, Barbara; Günthard, Huldrych F; Kivelä, Pia; Kouyos, Roger; Laeyendecker, Oliver; Liitsola, Kirsi; Meyer, Laurence; Porter, Kholoud; Ristola, Matti; van Sighem, Ard; Cornelissen, Marion; Kellam, Paul; Reiss, Peter

2018-01-01

Abstract Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between- and within-host diversity, including frequent indels, may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions. De novo assembly avoids this bias by aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the tool shiver to pre-process reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with the user’s choice of existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We used shiver to reconstruct the consensus sequence and minority variant information from paired-end short-read whole-genome data produced with the Illumina platform, for sixty-five existing publicly available samples and fifty new samples. We show the systematic superiority of mapping to shiver’s constructed reference compared with mapping the same reads to the closest of 3,249 real references: median values of 13 bases called differently and more accurately, 0 bases called differently and less accurately, and 205 bases of missing sequence recovered. We also successfully applied shiver to whole-genome samples of Hepatitis C Virus and Respiratory Syncytial Virus. shiver is publicly available from https://github.com/ChrisHIV/shiver. PMID:29876136

Overview of a multi-stakeholder dialogue around Shared Services for Health: the Digital Health Opportunity in Bangladesh.

PubMed

Ashraf, Sania; Moore, Carolyn; Gupta, Vaibhav; Chowdhury, Anir; Azad, Abul K; Singh, Neelu; Hagan, David; Labrique, Alain B

2015-12-09

National level policymaking and implementation includes multiple stakeholders with varied interests and priorities. Multi-stakeholder dialogues (MSDs) can facilitate consensus building through collective identification of challenges, recognition of shared goals and interests, and creation of solution pathways. This can shape joint planning and implementation for long-term efficiency in health and other sectors. Scaling up the effective use of information and communication technologies (ICTs) requires cohesive strategic planning towards a shared goal. In Bangladesh, the government and partners convened an MSD in March 2015 to increase stakeholder engagement in policymaking and implementation of a national ICT or electronic or mobile health (eHealth or mHealth) strategy, which seeks to incorporate ICTs into the national health system, aligning with the Digital Bangladesh Vision 2021. Relevant stakeholders were identified and key priorities and challenges were mapped through key informant interviews. An MSD was conducted with key stakeholders in Dhaka, Bangladesh. The MSD included presentations, group option generation, agreement and prioritization of barriers to scaling up ICTs. The MSD approach to building consensus on key priorities highlights the value of dialogue and collaboration with relevant stakeholders to encourage country ownership of nationwide efforts such as ICT scale-up. This MSD showed the dynamic context in which stakeholders operate, including those from academia, donors and foundations, healthcare professionals, associations, multilateral organizations, non-governmental organizations, partner countries and the private sector. Through this MSD, participants improved understanding of each other's contributions and interests, identified existing relationships, and agreed on policy and implementation gaps that needed to be filled. Collaboration among stakeholders in ICT efforts and research can promote a cohesive approach to scaling up, as well as improve policymaking by integrating interests and feedback of different key cross sectoral actors. MSDs can align stakeholders to identify challenges and solution pathways, and lead to coordinated action and accountability for resources and results. In addition, the MSD template and approach has been useful to guide ICT scale up in Bangladesh and could be replicated in other contexts to facilitate multi-constituency, multi-sector collaboration.

A Study of Parameters Affecting Fibroblast Morphology in Response to an Applied Mechanical Force

NASA Technical Reports Server (NTRS)

Grymes, Rosalind A.; Sawyer, Christine

1994-01-01

A precisely controlled stretch/relaxation regimen (20% elongation at 6.6 cycles/min) was applied to normal human fetal, neonatal and aged dermal fibroblasts cultured on flexible membranes. Culture conditions included poly (NH2) or collagen type I coated substrate membranes; control cultures were grown on the same pliable material in the absence of applied stretch. Direct observation and immunofluorescence analyses revealed a progressive change in cell body orientation limited to the stretched dermal fibroblast cultures. Monolayers gradually (over 4 days) acquired a symmetric, radial distribution equivalent to the biaxial array of the applied force. At high seeding density, alignment was inhibited in the fetal cell cultures. This cell strain required collagen type I coating for optimal attachment to the flexible membrane, preferring growth in three-dimensional cell 'balls' on the poly(NH2) coated substrate. Neonatal cells also required the collagen type I coating, but both neonatal and aged dermal fibroblasts aligned efficiently at all seeding densities examined. The randomly oriented neonatal cells on the unstretched control membranes spontaneously detached at confluence, as a single cell sheet. Their aligned counterparts did not detach until the applied stretch stimulus was removed. Low concentrations of cytochalasin D (62.5 ng/ml) disrupted the stretch-related alignment response. Rhodamine phalloidin staining visualized fewer actin stress fibers in stretched, aligned cells than in controls. Both intercellular interactions and cytoskeletal integrity mediate the response to mechanical strain. Normal rabbit corneal stroma fibroblasts (NRC) were also analyzed, and failed to orient under these conditions. This cell type may require a different regimen, or a longer time period, to demonstrate alignment behavior. Supported by NASA Space Biology RTOP 199-40-22 and the NASA-ARC Director's Discretionary Fund.

How Much Is Too Much Assessment? Insight into Assessment-Driven Student Learning Gains in Large-Scale Undergraduate Microbiology Courses

PubMed Central

Wang, Jack T. H.; Schembri, Mark A.; Hall, Roy A.

2013-01-01

Designing and implementing assessment tasks in large-scale undergraduate science courses is a labor-intensive process subject to increasing scrutiny from students and quality assurance authorities alike. Recent pedagogical research has provided conceptual frameworks for teaching introductory undergraduate microbiology, but has yet to define best-practice assessment guidelines. This study assessed the applicability of Biggs’ theory of constructive alignment in designing consistent learning objectives, activities, and assessment items that aligned with the American Society for Microbiology’s concept-based microbiology curriculum in MICR2000, an introductory microbiology course offered at the University of Queensland, Australia. By improving the internal consistency in assessment criteria and increasing the number of assessment items explicitly aligned to the course learning objectives, the teaching team was able to efficiently provide adequate feedback on numerous assessment tasks throughout the semester, which contributed to improved student performance and learning gains. When comparing the constructively aligned 2011 offering of MICR2000 with its 2010 counterpart, students obtained higher marks in both coursework assignments and examinations as the semester progressed. Students also valued the additional feedback provided, as student rankings for course feedback provision increased in 2011 and assessment and feedback was identified as a key strength of MICR2000. By designing MICR2000 using constructive alignment and iterative assessment tasks that followed a common set of learning outcomes, the teaching team was able to effectively deliver detailed and timely feedback in a large introductory microbiology course. This study serves as a case study for how constructive alignment can be integrated into modern teaching practices for large-scale courses. PMID:23858350

ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences.

PubMed

Bonizzoni, Paola; Rizzi, Raffaella; Pesole, Graziano

2005-10-05

Currently available methods to predict splice sites are mainly based on the independent and progressive alignment of transcript data (mostly ESTs) to the genomic sequence. Apart from often being computationally expensive, this approach is vulnerable to several problems--hence the need to develop novel strategies. We propose a method, based on a novel multiple genome-EST alignment algorithm, for the detection of splice sites. To avoid limitations of splice sites prediction (mainly, over-predictions) due to independent single EST alignments to the genomic sequence our approach performs a multiple alignment of transcript data to the genomic sequence based on the combined analysis of all available data. We recast the problem of predicting constitutive and alternative splicing as an optimization problem, where the optimal multiple transcript alignment minimizes the number of exons and hence of splice site observations. We have implemented a splice site predictor based on this algorithm in the software tool ASPIC (Alternative Splicing PredICtion). It is distinguished from other methods based on BLAST-like tools by the incorporation of entirely new ad hoc procedures for accurate and computationally efficient transcript alignment and adopts dynamic programming for the refinement of intron boundaries. ASPIC also provides the minimal set of non-mergeable transcript isoforms compatible with the detected splicing events. The ASPIC web resource is dynamically interconnected with the Ensembl and Unigene databases and also implements an upload facility. Extensive bench marking shows that ASPIC outperforms other existing methods in the detection of novel splicing isoforms and in the minimization of over-predictions. ASPIC also requires a lower computation time for processing a single gene and an EST cluster. The ASPIC web resource is available at http://aspic.algo.disco.unimib.it/aspic-devel/.

Prospects for School Mathematics. Seventy-Five Years of Progress.

ERIC Educational Resources Information Center

Carl, Iris M., Ed.

This book offers a broad view for a varied audience of what the vision expressed in all three National Council of Teachers of Mathematics' Standards documents will look like when aligned with practice and outlines ways in which desired changes can be realized. Six sections and 21 chapters in the book are: Section I--History: (1) "Paths to the…

A Preliminary Investigation into the Added Value of Multiple Gates and Informants in Universal Screening for Behavioral and Emotional Risk

ERIC Educational Resources Information Center

Dowdy, Erin; Dever, Bridget V.; Raines, Tara C.; Moffa, Kathryn

2016-01-01

Mental health screening in schools is a progressive practice to identify students for prevention and intervention services. Multiple gating procedures, in which students are provided more intensive assessments following initial identification of risk, are aligned with prevention science and poised to enhance multi-tiered systems of support. Yet,…

Power up Your Planning: A Well-Defined Theory of Action Leads to Systemwide Change

ERIC Educational Resources Information Center

Williams, Sharon; Cloninger, Karen

2018-01-01

Even though the West Linn-Wilsonville School District in Tualatin, Oregon was posting good results at all levels, when a new superintendent arrived, one of his first initiatives was to re-align progress from goals to a coherent system of professional development that would lead everyone to feel confident and competent in their work to reach all…

Race to the Top. Hawaii Report. Year 4: School Year 2013-2014. [State-Specific Summary Report

ERIC Educational Resources Information Center

US Department of Education, 2015

2015-01-01

This State-specific summary report serves as an assessment of Hawaii's Year 4 Race to the Top implementation. Hawaii made tremendous progress over the course of the grant period in implementing its Strategic Plan and six priority strategies and creating an aligned organization focused on increasing student outcomes. Among some of the other…

The PULSE Vision & Change Rubrics, Version 1.0: A Valid and Equitable Tool to Measure Transformation of Life Sciences Departments at All Institution Types

ERIC Educational Resources Information Center

Brancaccio-Taras, Loretta; Pape-Lindstrom, Pamela; Peteroy-Kelly, Marcy; Aguirre, Karen; Awong-Taylor, Judy; Balser, Teri; Cahill, Michael J.; Frey, Regina F.; Jack, Thomas; Kelrick, Michael; Marley, Kate; Miller, Kathryn G.; Osgood, Marcy; Romano, Sandra; Uzman, J. Akif; Zhao, Jiuqing

2016-01-01

The PULSE Vision & Change Rubrics, version 1.0, assess life sciences departments' progress toward implementation of the principles of the "Vision and Change report." This paper reports on the development of the rubrics, their validation, and their reliability in measuring departmental change aligned with the "Vision and…

Alignment Content Analysis of NAEP 2009 Reading Assessment Analysis Based on Method of Surveys of Enacted Curriculum

ERIC Educational Resources Information Center

Blank, Rolf K.; Smithson, John

2010-01-01

Beginning in summer 2009, the complete set of NAEP student assessment items for grades 4 and 8 Science and Reading 2009 assessments were analyzed for comparison to the National Assessment of Educational Progress (NAEP) Item Specifications which are based on the NAEP Assessment Frameworks for these subjects (National Assessment Governing Board,…

From Pipelines to Partnerships: A Synthesis of Research on How Diverse Families, Schools, and Communities Support Children's Pathways Through School

ERIC Educational Resources Information Center

Cooper, Catherine R.; Chavira, Gabriela; Mena, Dolores D.

2005-01-01

This article maps recent progress on 5 key questions about "the academic pipeline problem" of different rates of persistence through school among ethnically diverse students across the nation. The article shows the complementary development of the Overlapping Spheres of Influence Theory and Sociocultural Theory and aligns concepts and measures…

Aligning Coordination Class Theory with a New Context: Applying a Theory of Individual Learning to Group Learning

ERIC Educational Resources Information Center

Barth-Cohen, Lauren A.; Wittmann, Michael C.

2017-01-01

This article presents an empirical analysis of conceptual difficulties encountered and ways students made progress in learning at both individual and group levels in a classroom environment in which the students used an embodied modeling activity to make sense of a specific scientific scenario. The theoretical framework, coordination class theory,…

Applying the collective impact approach to address non-native species: A case study of the Great Lakes Phragmites Collaborative

USGS Publications Warehouse

Braun, H. B.; Kowalski, Kurt P.; Hollins, K.

2016-01-01

To address the invasion of non-native Phragmites in the Great Lakes, researchers at the U.S. Geological Survey—Great Lakes Science Center partnered with the Great Lakes Commission in 2012 to establish the Great Lakes Phragmites Collaborative (GLPC). The GLPC is a regional-scale partnership established to improve collaboration among stakeholders and increase the effectiveness of non-native Phragmites management and research. Rather than forming a traditional partnership with a narrowly defined goal, the GLPC follows the principles of collective impact to engage stakeholders, guide progress, and align resources to address this complex, regional challenge. In this paper, the concept and tenets of collective impact are described, the GLPC is offered as a model for other natural resource-focused collective impact efforts, and steps for establishing collaboratives are presented. Capitalizing on the interactive collective impact approach, the GLPC is moving toward a broadly accepted common agenda around which agencies and individuals will be able to better align their actions and generate measureable progress in the regional campaign to protect healthy, diverse ecosystems from damage caused by non-native Phragmites.

Defining a set of standardised outcome measures for newly diagnosed patients with multiple myeloma using the Delphi consensus method: the IMPORTA project.

PubMed

Blade, Joan; Calleja, Miguel Ángel; Lahuerta, Juan José; Poveda, José Luis; de Paz, Héctor David; Lizán, Luis

2018-02-22

To define a standard set of outcomes and the most appropriate instruments to measure them for managing newly diagnosed patients with multiple myeloma (MM). A literature review and five discussion groups facilitated the design of two-round Delphi questionnaire. Delphi panellists (haematologists, hospital pharmacists and patients) were identified by the scientific committee, the Spanish Program of Haematology Treatments Foundation, the Spanish Society of Hospital Pharmacies and the Spanish Community of Patients with MM. Panellist's perception about outcomes' suitability and feasibility of use was assessed on a seven-point Likert scale. Consensus was reached when at least 75% of the respondents reached agreement or disagreement. A scientific committee led the project. Fifty-one and 45 panellists participated in the first and second Delphi rounds, respectively. Consensus was reached to use overall survival, progression-free survival, minimal residual disease and treatment response to assess survival and disease control. Panellists agreed to measure health-related quality of life, pain, performance status, fatigue, psychosocial status, symptoms, self-perception on body image, sexuality and preferences/satisfaction. However, panellist did not reach consensus about the feasibility of assessing in routine practice psychosocial status, symptoms, self-perception on body image and sexuality. Consensus was reached to collect patient-reported outcomes through the European Organisation for the Research and Treatment of Cancer (EORTC) Quality of Life Questionnaire (QLQ) Core questionnaire 30 (C30), three items from EORTC-QLQ-Multiple Myeloma (MY20) and EORTC-QLQ-Breast Cancer (BR23), pain Visual Analogue Scale, Morisky-Green and ad hoc questions about patients' preferences/satisfaction. A consensual standard set of outcomes for managing newly diagnosed patients with MM has been defined. The feasibility of its implementation in routine practice will be assessed in a future pilot study. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Clinicopathologic consensus study of gray zone lymphoma with features intermediate between DLBCL and classical HL.

PubMed

Pilichowska, Monika; Pittaluga, Stefania; Ferry, Judith A; Hemminger, Jessica; Chang, Hong; Kanakry, Jennifer A; Sehn, Laurie H; Feldman, Tatyana; Abramson, Jeremy S; Kritharis, Athena; Hernandez-Ilizaliturri, Francisco J; Lossos, Izidore S; Press, Oliver W; Fenske, Timothy S; Friedberg, Jonathan W; Vose, Julie M; Blum, Kristie A; Jagadeesh, Deepa; Woda, Bruce; Gupta, Gaurav K; Gascoyne, Randy D; Jaffe, Elaine S; Evens, Andrew M

2017-12-12

Gray zone lymphoma (GZL) is described as sharing features with classical Hodgkin lymphoma (cHL) and diffuse large B-cell lymphoma (DLBCL). However, there remains complexity in establishing diagnosis, delineating prognosis, and determining optimum therapy. Sixty-eight cases diagnosed as GZL across 15 North American academic centers were evaluated by central pathology review to achieve consensus. Of these, only 26 (38%) were confirmed as GZL. Morphology was critical to GZL consensus diagnosis (eg, tumor cell richness); immunohistochemistry showed universal B-cell derivation, frequent CD30 expression, and rare Epstein-Barr virus (EBV) positivity (CD20 + , 83%; PAX5 + , 100%; BCL6 + , 20%; MUM1 + , 100%; CD30 + , 92%; EBV + , 4%). Forty-two cases were reclassified: nodular sclerosis (NS) cHL, n = 27 (including n = 10 NS grade 2); lymphocyte predominant HL, n = 4; DLBCL, n = 4; EBV + DLBCL, n = 3; primary mediastinal large BCL n = 2; lymphocyte-rich cHL and BCL-not otherwise specified, n = 1 each. GZL consensus-confirmed vs reclassified cases, respectively, more often had mediastinal disease (69% vs 41%; P = .038) and less likely more than 1 extranodal site (0% vs 25%; P = .019). With a 44-month median follow-up, 3-year progression-free survival (PFS) and overall survival for patients with confirmed GZL were 39% and 95%, respectively, vs 58% and 85%, respectively, for reclassified cases ( P = .19 and P = .15, respectively). Interestingly, NS grade 2 reclassified patients had similar PFS as GZL consensus-confirmed cases. For prognostication of GZL cases, hypoalbuminemia was a negative factor (3-year PFS, 12% vs 64%; P = .01), whereas frontline cyclophosphamide, doxorubicin, vincristine, and prednisone ± rituximab (CHOP±R) was associated with improved 3-year PFS (70% vs 20%; P = .03); both factors remained significant on multivariate analysis. Altogether, accurate diagnosis of GZL remains challenging, and improved therapeutic strategies are needed.

Clinicopathologic consensus study of gray zone lymphoma with features intermediate between DLBCL and classical HL

PubMed Central

Pilichowska, Monika; Pittaluga, Stefania; Ferry, Judith A.; Hemminger, Jessica; Chang, Hong; Kanakry, Jennifer A.; Sehn, Laurie H.; Feldman, Tatyana; Abramson, Jeremy S.; Kritharis, Athena; Hernandez-Ilizaliturri, Francisco J.; Lossos, Izidore S.; Press, Oliver W.; Fenske, Timothy S.; Friedberg, Jonathan W.; Vose, Julie M.; Blum, Kristie A.; Jagadeesh, Deepa; Woda, Bruce; Gupta, Gaurav K.; Gascoyne, Randy D.; Jaffe, Elaine S.

2017-01-01

Gray zone lymphoma (GZL) is described as sharing features with classical Hodgkin lymphoma (cHL) and diffuse large B-cell lymphoma (DLBCL). However, there remains complexity in establishing diagnosis, delineating prognosis, and determining optimum therapy. Sixty-eight cases diagnosed as GZL across 15 North American academic centers were evaluated by central pathology review to achieve consensus. Of these, only 26 (38%) were confirmed as GZL. Morphology was critical to GZL consensus diagnosis (eg, tumor cell richness); immunohistochemistry showed universal B-cell derivation, frequent CD30 expression, and rare Epstein-Barr virus (EBV) positivity (CD20+, 83%; PAX5+, 100%; BCL6+, 20%; MUM1+, 100%; CD30+, 92%; EBV+, 4%). Forty-two cases were reclassified: nodular sclerosis (NS) cHL, n = 27 (including n = 10 NS grade 2); lymphocyte predominant HL, n = 4; DLBCL, n = 4; EBV+ DLBCL, n = 3; primary mediastinal large BCL n = 2; lymphocyte-rich cHL and BCL–not otherwise specified, n = 1 each. GZL consensus-confirmed vs reclassified cases, respectively, more often had mediastinal disease (69% vs 41%; P = .038) and less likely more than 1 extranodal site (0% vs 25%; P = .019). With a 44-month median follow-up, 3-year progression-free survival (PFS) and overall survival for patients with confirmed GZL were 39% and 95%, respectively, vs 58% and 85%, respectively, for reclassified cases (P = .19 and P = .15, respectively). Interestingly, NS grade 2 reclassified patients had similar PFS as GZL consensus-confirmed cases. For prognostication of GZL cases, hypoalbuminemia was a negative factor (3-year PFS, 12% vs 64%; P = .01), whereas frontline cyclophosphamide, doxorubicin, vincristine, and prednisone ± rituximab (CHOP±R) was associated with improved 3-year PFS (70% vs 20%; P = .03); both factors remained significant on multivariate analysis. Altogether, accurate diagnosis of GZL remains challenging, and improved therapeutic strategies are needed. PMID:29296913